Thermo Fisher Scientific GeneMapper™ Software User guide

GeneMapper™ Software

Version 3.5

User Guide

For Research Use Only. Not for use in diagnostic procedures.

Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that

may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall

Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use

of this document.

Notice to Purchaser: License Disclaimer.

Purchase of this software product alone does not imply any license under any process, instrument or other apparatus,

system, composition, reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation, either

expressly, or by estoppel.

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, and SNaPshot are registered trademarks, and the AB Design, Applera, GeneMapper, GeneScan,

SNPlex, and ZipChute are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries.

AppleScript and Macintosh are registered trademarks of Apple Computer, Inc.

reserved.

Microsoft Windows NT and Microsoft Excel are registered trademarks 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.

All other trademarks are the sole property of their respective owners.

Part Number 4343790 Rev. B

10/2003

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Contents

GeneMapper™ Software v3.5 User Guide iii

Preface How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii

Contacting Applied Biosystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii

Chapter 1 Getting Started

New Features in v3.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2

Before You Install v3.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3

GeneMapper Software Flowchart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5

Logging Into GeneMapper Software for the First Time . . . . . . . . . . . . 1-6

Logging Into and Out of the GeneMapper Software . . . . . . . . . . . . . . . 1-8

Window Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11

Chapter 2 Auditing and Software Access Control

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2

Access Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3

Administration Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4

Creating a New User . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9

Creating a New Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12

Security Settings on Multiple Computers . . . . . . . . . . . . . . . . . . . . . . 2-15

Audit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-17

Audit Map Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-21

Audit History Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-25

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iv GeneMapper™ Software v3.5 User Guide

Chapter 3 Archiving Data

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

Starting the Archiver Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

Exiting the Archiver Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

Archiver Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3

Archiving Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

Archiving and Restoring Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7

Creating and Submitting an Archive Request . . . . . . . . . . . . . . . . . . . 3-8

Restoring Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9

Searching for Objects to Archive . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-11

Searching for Objects to Restore . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13

Viewing Archive Locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15

Viewing Archive Requests and Restore Requests . . . . . . . . . . . . . . . 3-16

Chapter 4 Software Functions

GeneMapper Software Genotyping Algorithms . . . . . . . . . . . . . . . . . . 4-2

Peak Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3

Optimizing Peak Detection Sensitivity . . . . . . . . . . . . . . . . . . . . . . . . . 4-6

Slope Thresholds for Peak Start and Peak End Parameters . . . . . . . 4-11

Slope Threshold Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-13

Size-Match/Size-Calling Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . 4-15

Size Calling Methods for Classic and Advanced Modes . . . . . . . . . . 4-16

Allele-Calling Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-22

Component-Based Quality Values (PQV) . . . . . . . . . . . . . . . . . . . . . . 4-24

Process Quality Value Determination . . . . . . . . . . . . . . . . . . . . . . . . . 4-25

Chapter 5 Example Workflows

General Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2

Sizing Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2

Microsatellite Workflow (Sizing Only) . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3

Auto Panel Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4

OLA_Analysis Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5

SNPlex™ Kit Assays Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6

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GeneMapper™ Software v3.5 User Guide v

Glossary

Index

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vi GeneMapper™ Software v3.5 User Guide

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GeneMapper™ Software v3.5 User Guide vii

Preface

How to Use This Guide

Purpose of This

Guide The Applied Biosystems GeneMapper™ Software v3.5 User Guide

provides procedures for the using the software features.

Audience This guide is intended for trained laboratory personnel. Applied

Biosystems is not liable for damage or injury that results from use of

this guide by unauthorized or untrained parties.

Text Conventions This guide uses the following conventions:

•Bold indicates user action. For example:

Ty pe 0, then press Enter for each of the remaining fields.

•Italic text indicates new or important words and is also used for

emphasis. For example:

Before analyzing, always prepare fresh matrix.

• A right arrow bracket (>) separates successive commands you

select from a drop-down or shortcut menu. For example:

Select File > Open > Spot Set.

Right-click the sample row, then select View Filter > View All

Runs.

User Attention

Words Two user attention words appear in Applied Biosystems user

documentation. Each word implies a particular level of observation

or action as described below:

Note: Provides information that may be of interest or help but is not

critical to the use of the product.

IMPORTANT! Provides information that is necessary for proper

instrument operation, accurate chemistry kit use, or safe use of a

chemical.

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Preface

viii GeneMapper™ Software v3.5 User Guide

How to Obtain More Information

help by pressing F1 on the keyboard or from the Help drop-

menu on the toolbar.

•GeneMapper™ Software v3.5 Installation Guide PN 4344950.

Contacting Applied Biosystems

How to Obtain

Services and

Support

To contact Applied Biosystems Technical Support from North

America by telephone, call 1.800.899.5858.

For the latest services and support information for all locations, go to

http://www.appliedbiosystems.com, then click the link

for Support.

At the Services and Support page, you can:

• Search through frequently asked questions (FAQs)

• Submit a question directly to Technical Support

• Order Applied Biosystems user documents, MSDSs, certificates

of analysis, and other related documents

• Download PDF documents

• Obtain information about customer training

• Download software updates and patches

In addition, the Services and Support page provides access to

worldwide telephone and fax numbers to contact Applied Biosystems

Technical Support and Sales facilities.

Send Us Your

Comments Applied Biosystems welcomes your comments and suggestions for

improving user documents. You can e-mail your comments to:

techpubs@appliedbiosystems.com

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Contacting Applied Biosystems

GeneMapper™ Software v3.5 User Guide ix

Troubleshooting

Checklist Complete the troubleshooting checklist before contacting Technical

Support:

Table 1 Troubleshooting Checklist

Check Information for Technical Support

Summarize the problem:

Have you been able to repeat the problem?

If yes, list the steps that you perform:

1.

2.

3.

4.

5.

6.

Applied Biosystems personnel that you have contacted:

❏Field Applications Specialist

❏Field Service Engineer

❏Technical Support

❏Sales Representative

❏Order Administration

❏Other

Computer specifications:

• Operating system:

•Version:

• Processor

•Memory

• Hard disk space:

• Hard disk configuration:

Software installed:

❏Data Collection Software v__

❏Status of Data Collection Services____

❏GeneMapper Software v__

❏Other Applied Biosystems software:

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Preface

x GeneMapper™ Software v3.5 User Guide

Computer login information:

• User privileges:

• Local or networked domain:

Software configuration installed:

❏Instrument

❏Remote autoanalysis

❏Standalone

Instrument and instrument computer information:

•Model:

• Data Collection Software v__

• Status of Data Collection Services____

• Other Applied Biosystems software:

• Capillary length:

• Capillary lot number:

• Run module:

•Dye set:

Chemistry kit or reagent, with version number:

Be prepared to send to Technical Support:

• Installation log files

• Exported panels

• Exported bins

• Exported size standard definition

• Exported analysis method

• Sample (.fsa) files

• GeneMapper_log.txt

• PanelImportLog.txt

•Printed results

Table 1 Troubleshooting Checklist (continued)

Check Information for Technical Support

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GeneMapper™ Software v3.5 User Guide 1-1

1

Getting Started 1

This chapter covers:

New Features in v3.5. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-2

Before You Install v3.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-3

GeneMapper Software Flowchart . . . . . . . . . . . . . . . . . . . . . . . . . .1-6

Logging Into GeneMapper Software for the First Time . . . . . . . . .1-7

Logging Into and Out of the GeneMapper Software. . . . . . . . . . . .1-9

Window Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-13

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Chapter 1 Getting Started

1-2 GeneMapper™ Software v3.5 User Guide

New Features in v3.5

• Access control and auditing

• Automated analysis with ABI Prism® 3100/3100-Avant Genetic

Analyzers

• Remote analysis

• New features and functions for analysis using the SNPlex™

Genotyping System:

– Cluster plot analysis and display for SNP genotyping

– New assay-specific Process (Component-Based) Quality

Values (PQVs)

• OLA_Analysis analysis method for certain oligo ligation assay

(OLA)-based mutation analysis

• Improved analysis and post-analysis functions:

– Improved plots performance speed

– Improved printing speeds and views

• Drag-and-drop marker management

• Database archiving

• Database management

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Before You Install v3.5

GeneMapper™ Software v3.5 User Guide 1-3

Before You Install v3.5

Computer

Requirements For optimal performance of the software, install the software on a

computer with:

• 2.4 GHz Intel® Pentium® 4 processor

• 1 GB of RAM

• Two 120 GB hard drives

• 20/48x IDE CD-ROM

• 10/100 NIC with RWU (internal)

• 17" color monitor

• Microsoft® Windows® 2000 Professional, Service Pack 3.

Important Notes Note: Applied Biosystems ships the Dell Precision™ Workstation

340. The Dell 340 computer that shipped with the

Applied Biosystems 3730/3730xl DNA Analyzers Data Collection

Software v1.0 is sufficient but does not provide optimal performance.

Note: GeneMapper software is not compatible with dual-processors

or with Intel® Xeon™ processors.

Note: For optimal performance of GeneMapper software, partition

the hard drives on your computer.

Note: The Oracle™ database version in GeneMapper™ Software v3.0

is an embedded license database. This license allows access to the

database for 5 named users at any given time. To accommodate more

than 5 named users, you should either purchase additional

GeneMapper™ Software licenses or, purchase additional Oracle

named user privileges and thereby, honoring Applied Biosystems’

agreement with Oracle™.

Supported

Instruments The GeneMapper™ Software v3.5 supports data generated on the

following instruments:

• Applied Biosystems 3730 DNA Analyzer

• Applied Biosystems 3730xl DNA Analyzer

• ABI PRISM® 3100 Genetic Analyzer

• ABI PRISM® 3100-Avant Genetic Analyzer

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Chapter 1 Getting Started

1-4 GeneMapper™ Software v3.5 User Guide

Data Collection

Software

Compatibility

Supported

Fragment

Analysis

Chemistry Kits

The GeneMapper™ Software v3.5 is designed to analyze the data

generated using several fragment analysis chemistry kits on the

Applied Biosystems 3730 DNA Analyzer, Applied Biosystems

3730xl 3730 DNA Analyzer, ABI PRISM® 3100 Genetic Analyzer,

and/or ABI PRISM® 3100-Avant Genetic Analyzer systems.

Kits Supported Using the 3730 or 3730xl Systems

• ABI PRISM® GeneScan™ Size Standards (LIZ® dye only)

• ABI PRISM® Linkage Mapping Set v2.5

• ABI PRISM® Mouse Mapping Primers v1.0

•SNPlex

™ Genotyping System (new for v3.5)

• Custom microsatellites (G5 dye set only)

Note: Analysis of non-STR applications, including AFLP, SSCP, and

polyploidy data, is not supported.

Kits Supported Using the 3100 or 3100-Avant Systems

• ABI PRISM® GeneScan™ Size Standards (ROX™ dye, LIZ® dye)

• ABI PRISM® Linkage Mapping Set v2.5

• ABI PRISM® Mouse Mapping Primers v1.0

• ABI PRISM® SNaPshot® Multiplex Kit

• ABI PRISM® SNaPshot® Primer Focus™ Kit

•SNPlex

™ Genotyping System (new for v3.5)

•StockMarks

® Animal Parentage Typing Kits

• Custom microsatellites

• Certain oligo ligation assay (OLA)-based mutation analysis

assays

Note: Analysis of non-STR applications, including AFLP, SSCP, and

polyploidy data, is not supported.

Table 1-1 Functional compatibility between GeneMapper™

Software v3.5 and Data Collection Software v1.0 and v2.0

Data Collection

Software Version Sample File

Compatibility Co-installation and

Autoanalysis

2.0 Yes Yes

1.0 No No

GeneMapper Software Flowchart

GeneMapper Software v3.5 User Guide 1-5

GeneMapper Software Flowchart

G

e

n

e

M

a

p

e

r

@

S

o

f

t

w

a

r

e

Secondary

database DeleteCD

Log

Analyze

Projects

Table settings

Plot settings

Export to

*.ser, *.txt Print

Apply

Create,

import, or edit

Apply

panels

Examine

Results

Set Up

Fragment Analysis

Samples plot

Genotypes plot

Samples table

Genotypes table

Cluster plot

Raw data

Size standards

Sample files

DNA analyzers

.fsa

Create,

import,

or edit

Projects

Kits,

panels,

markers,

bins

Kits,

panels,

binsets

Analysis methods

Size standards

SNP sets

Table settings

Plot settings

Analysis methods

Size standards

SNP sets

G

e

n

e

M

a

p

e

r

D

a

t

a

b

a

s

e

Import/export

Import/

export

Import/

export

Auditing

Access Control

Archive

GeneMapper Manager

Panel Manager

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Chapter 1 Getting Started

1-6 GeneMapper™ Software v3.5 User Guide

Logging Into GeneMapper Software for the First

Time

Installation For installation procedures, refer to the GeneMapper™ Software v3.5

Installation Guide PN 4344950.

Logging in for the

First Time The first time that you log into the software, use the default user

name and change the password.

To log in for the first time:

1. Enter:

a. User Name: gm

b. Password: password

2. Click OK to display the Password Change Required dialog box.

Since the password is pre-expired you are required to it on first

login.

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Logging Into GeneMapper Software for the First Time

GeneMapper™ Software v3.5 User Guide 1-7

3. Click OK to display the Change Password Dialog box.

4. Type a new password, retype the new password to confirm, and

click OK.

5. Two license agreements display during the first login. Click

Accept for each and a new, untitled Project window displays.

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Chapter 1 Getting Started

1-8 GeneMapper™ Software v3.5 User Guide

Logging Into and Out of the GeneMapper Software

Logging into the

Computer Installing the GeneMapper software v3.5 on the computer requires

that you log into the computer:

• As the administrator

• Into the local domain

IMPORTANT! Do not log on to the network.

Logging into

GeneMapper

Software

To log into the GeneMapper software:

1. Start the GeneMapper software.

2. Select your user name from the User Name drop-list or, if your

name is not listed there, type it in.

If you do not have a User Name, request a user name and/or

password from the Administrator. If you are the Administrator,

use:

–User Name: Administrator

–Password: Administrator

If your password is pre-expired, you are prompted to create a

password when you click OK.

3. Enter your password.

4. Click OK.

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Logging Into and Out of the GeneMapper Software

GeneMapper™ Software v3.5 User Guide 1-9

Note: If you unsuccessfully attempt to log into the software

more times than allowed by your password policy, your account

becomes “suspended.” You must wait a the amount of time

specified by your policy or ask your administrator to change

back your status to “active.”

Connecting to a

New Host To connect to a new host:

1. Click New Host on the Login to GeneMapper dialog box.

The New Host dialog box displays.

This option allows you to connect to GeneMapper software v3.5

databases on other computers.

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Chapter 1 Getting Started

1-10 GeneMapper™ Software v3.5 User Guide

2. In the Host Name field, enter the machine name or IP address of

the database host.

The window displays the new database host and its user names

list. If the GeneMapper software cannot connect to the database

host you entered, the following error message opens: “You have

entered an invalid host.” Click OK to exit and reenter the

database host information.

3. Select the appropriate machine type from the drop-down list.

4. Click OK.

IMPORTANT! If, at any point, the network connection is interrupted

or lost, GeneMapper software becomes unusable. You must then exit

the software and restart it.

Logging Out Close the GeneMapper software in one of three ways:

•Click File > Logout, or

•Click File > Exit, or

•Click the Close button .

If you close GeneMapper software with a new or blank Project

window (or no changes in your Project), the Save Project (logout)

dialog box does not open.

When you log out of the GeneMapper software, you have the option

of saving or discarding the changes you made since the last time you

updated the project.

If you close the GeneMapper software using the Logout command,

the login window reopens after you select either “Yes” or “No”.

GeneMapper software closes completely if you use either the Exit

command or the Close button.

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Thermo Fisher Scientific GeneMapper™ Software User guide

Thermo Fisher Scientific GeneMapper™ Software User guide

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