Thermo Fisher Scientific Applied Biosystems SOLiD 3 System: SOLiD Experimental Tracking Software Owner's manual

Getting Started Guide

Applied Biosystems SOLiD™ 3 System

SETS v3.0 Getting Started Guide

SOLiD Experimental Tracking Software (SETS)

Getting Started Guide

Applied Biosystems SOLiD™ 3 System

SETS v3.0 Getting Started Guide

SOLiD Experimental Tracking Software (SETS)

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

This user guide is the proprietary material of Life Technologies or its subsidiaries and is protected by laws of copyright. The

customer of the SOLiD™ 3 System is hereby granted limited, non-exclusive rights to use this user guide solely for the purpose of

operating the SOLiD™ 3 System. Unauthorized copying, renting, modifying, or creating derivatives of this user guide is

prohibited.

Information in this document is subject to change without notice.

APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR

PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL APPLIED BIOSYSTEMS BE

LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR

SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH

OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF, WHETHER OR NOT

FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH

DAMAGES.

TRADEMARKS:

Life Technologies, Applied Biosystems, AB (Design) and GeneAmp are registered trademarks and MicroAmp and SOLiD are

trademarks of Applied Biosystems LLC, or its subsidiaries in the US and/or certain other countries.

Covaris is a trademark of Covaris, Inc.

AmpliTaq and AmpliTaq Gold are registered trademarks of Roche Molecular Systems, Inc.

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

Part Number 4389302 Rev. C

02/2009

iii

SOLiD™ 3 System – SETS v3.0 Getting Started Guide

Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Safety information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

How to use this guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii

How to obtain support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

Chapter 1 SETS Software Overview . . . . . . . . . . . . . . . . . . . . . . . 1

SOLiD™ 3 System Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

SETS Software Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

SETS Homepage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Chapter 2 Prepare Run Settings . . . . . . . . . . . . . . . . . . . . . . . . . . 7

ICS and SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

SOLiD™ 3 System Software Workflow Relationship . . . . . . . . . . . . . . . . . 9

Log In to SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Set Analysis Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Load a Reference Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Chapter 3 Monitor the Run in SETS . . . . . . . . . . . . . . . . . . . . . . 27

View Run Metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

View Cycle Scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

View Sample Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Troubleshoot Failed Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

View History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Cancel Analysis Midstream . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Cluster Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

System Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

RSS Feed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

iv SOLiD™ 3 System – SETS v3.0 Getting Started Guide

Contents

Chapter 4 View Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

View Overall Run Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

View Sample Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

View Analysis Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Master Report Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

Chapter 5 Perform Reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Primary Reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Secondary Reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Chapter 6 Support Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . . 93

Multiplexing and Barcodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

View Multiplexing Series in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

Setup a Multiplexing Run in ICS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96

Multiplexing Series Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

Chapter 7 Manage Administrative Tasks . . . . . . . . . . . . . . . . . 101

Global SETS and Export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

Auto-Export in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Manual Export in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

Event Notifications and Email Services . . . . . . . . . . . . . . . . . . . . . . . . 109

Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112

Delete Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

Manage Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

Appendix A Web Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

Appendix B Software License Agreement . . . . . . . . . . . . . . . . . . 119

Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

Contents

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SOLiD™ 3 System – SETS v3.0 Getting Started Guide

Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

vi SOLiD™ 3 System – SETS v3.0 Getting Started Guide

Contents

vii

SOLiD™ 3 System – SETS v3.0 Getting Started Guide

Preface

Safety information

Note: For general safety information, see this Preface and

Appendix C, “Safety” on page 117. When a hazard symbol and

hazard type appear by a chemical name or instrument hazard, see the

“Safety” Appendix for the complete alert on the chemical or

instrument.

Safety alert words Four safety alert words appear in Applied Biosystems user

documentation at points in the document where you need to be aware

of relevant hazards. Each alert word—IMPORTANT, CAUTION,

WARNING, DANGER—implies a particular level of observation or

action, as defined below:

IMPORTANT! – Indicates information that is necessary for proper

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

chemical.

CAUTION! – Indicates a potentially hazardous situation that,

if not avoided, may result in minor or moderate injury. It may

also be used to alert against unsafe practices.

WARNING! – Indicates a potentially hazardous situation that,

if not avoided, could result in death or serious injury.

DANGER! – Indicates an imminently hazardous situation

that, if not avoided, will result in death or serious injury. This

signal word is to be limited to the most extreme situations.

Preface

How to use this guide

viii SOLiD™ 3 System – SETS v3.0 Getting Started Guide

How to use this guide

Text conventions This guide uses the following conventions:

•Bold text 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 symbol () 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.

Preface

How to obtain support

ix

SOLiD™ 3 System – SETS v3.0 Getting Started Guide

How to obtain support

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

to:

www.appliedbiosystems.com

At the Applied Biosystems web site, you can:

• Access worldwide telephone and fax numbers to contact

Applied Biosystems Technical Support and Sales facilities.

• 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.

Preface

How to obtain support

xSOLiD™ 3 System – SETS v3.0 Getting Started Guide

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Chapter 1

1

SOLiD™ 3 System – SETS Software Getting Started Guide

SETS Software Overview

This chapter covers:

■SOLiD™ 3 System Overview . . . . . . . . . . . . . . . . . . . . . . . . . 2

■SETS Software Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

■SETS Homepage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

SETS Software Overview

Prepare Run Settings

Monitor the Run in SETS

View Reports

Perform Reanalysis

Support Multiplexing

Manage Administrative Tasks

Chapter 1 SETS Software Overview

SOLiD™ 3 System Overview1

2SOLiD™ 3 System – SETS Software Getting Started Guide

SOLiD™ 3 System Overview

SOLiD™

Technology

The Applied Biosystems SOLiD™ 3 System provides parallel

sequencing of clonally amplified DNA fragments linked to magnetic

beads. The sequencing methodology is based on sequential ligation

with dye-labeled oligonucleotides. All fluorescently labeled

oligonucleotide probes are present simultaneously, competing for

incorporation. After each ligation, fluorescence is measured before

another round of ligation takes place.

This ligation-based chemistry eliminates dephasing. The use of a

two-base encoding mechanism, which interrogates each base twice

for errors during sequencing, discriminates between true

polymorphisms and system noise. The SOLiD™ Analyzer software

allows customers to monitor the runs in real-time, and provides basic

data analysis tools.

The SOLiD™ 3 System consists of:

•SOLiD

™ Analyzer

• All ancillary equipment

• ICS software, which is described in the Applied Biosystems

SOLiD™ 3 System Instrument Operation Guide (PN 4402739)

•SOLiD

™ Experiment Tracking System (SETS) software, which

is described in this document

Chapter 1 SETS Software Overview

SETS Software Overview 1

3

SOLiD™ 3 System – SETS Software Getting Started Guide

SETS Software Overview

Overview The SOLiD™ Experiment Tracking System (SETS) software is a

web-based application for viewing real-time data and completed run

analysis reports from a SOLiD™ Analyzer. The SOLiD™ Analyzer

system uses ligation-based sequencing, then filters data to remove

missing calls, nonligations, and/or redundancies.

Data are analyzed at two levels:

• Primary analysis, which involves:

– Image alignment

– Color assignment

– Color calls

– Quality value assignments

• Secondary analysis, which compares color space calls to a

reference sequence

Opening SETS When using the SOLiD™ Analyzer computer, you can access SETS

by:

• Typing in the SETS software URL, supplied by the Applied

Biosystems Field Service Engineer:

This address opens the SETS software to the homepage and you are

automatically logged-in as a “guest” user. As a guest, you can only

view analyzed data and reports. Log in to the software to perform

other functions. See “Log In to SETS” on page 10.

Chapter 1 SETS Software Overview

SETS Homepage1

4SOLiD™ 3 System – SETS Software Getting Started Guide

SETS Homepage

The SETS software opens to the homepage where you can view real-

time and completed-run data generated by the SOLiD™ Analyzer.

The homepage is divided into three sections:

• Error Messages

• In-Progress or Most Recent Runs (per flowcell)

• Recent Analyses

At the upper left-hand corner, you can see the current login

information, including instrument name and SETS user:

Chapter 1 SETS Software Overview

SETS Homepage 1

5

SOLiD™ 3 System – SETS Software Getting Started Guide

Error Messages When there are error messages, the Log Messages section displays

them at the top of the homepage. You can scroll through the

messages or click to remove all messages from the field.

For more information on log messages, see Chapter 3, System Logs.

In Progress or Most

Recent Run

This section displays status of a current run or results for the most

recently completed run. Flowcell 1 displays on the left-hand side of

the window; flowcell 2 displays on the right side.

To understand more about your run, click or More

Information within each flowcell section.

Chapter 1 SETS Software Overview

SETS Homepage1

6SOLiD™ 3 System – SETS Software Getting Started Guide

Run Metrics provides quality metrics in the form of traffic lights to

help you assess the progress and measurable quality of the run. More

Information allows you to view analyzed data for a particular run.

For details on monitoring a run, see Chapter 3, Monitor the Run in

SETS.

Note: At any time you can return to the SETS homepage by clicking

the button on the main menu at the top of the screen.

Recent Analyses This section displays the progress of data analysis for individual

samples.

For every analysis, you can see:

• run name

• sample name

• date created

• last closed stage

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Chapter 2

7

SOLiD™ 3 System – SETS Software Getting Started Guide

Prepare Run Settings

This chapter covers:

■ICS and SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

■SOLiD™ 3 System Software Workflow Relationship. . . . . . . . 9

■Log In to SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

■Set Analysis Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

■Load a Reference Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . 25

SETS Software Overview

Prepare Run Settings

Monitor the Run in SETS

View Reports

Perform Reanalysis

Support Multiplexing

Manage Administrative Tasks

Chapter 2 Prepare Run Settings

ICS and SETS2

8SOLiD™ 3 System – SETS Software Getting Started Guide

ICS and SETS

To understand the relationship of the two software components in the

SOLiD™ 3 System and how a user would interact between the two in

a typical workflow, refer to the “SOLiD™ 3 System Software

Workflow Relationship” on page 9.

Analysis Settings Before you start a run on the SOLiD™ Analyzer using the

Instrument Control Software (ICS), open the SETS software and

select the secondary analysis settings. To use a reference sequence

not listed in the drop-down list, upload your reference and add it to

the list. For details, see:

•“Set Analysis Parameters” on page 11

•“Load a Reference Sequence” on page 25

Secondary analysis (sequence data alignments to a reference

sequence) will not occur without a preloaded reference sequence.

IMPORTANT! For more complex genomes, such as the human

genome, secondary analysis should occur on a different cluster from

the one that controls the SOLiD™ 3 System. Sequencing data from

complex genomes are often analyzed in smaller batches, for instance,

one chromosome at a time.

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Thermo Fisher Scientific Applied Biosystems SOLiD 3 System: SOLiD Experimental Tracking Software Owner's manual

Thermo Fisher Scientific Applied Biosystems SOLiD 3 System: SOLiD Experimental Tracking Software Owner's manual

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