Roche AMPLILINK 3 User manual

Application Manual

Version 1.1

For use with

COBAS

®

AmpliPrep instrument,

COBAS

®

TaqMan

®

analyzer,

COBAS

®

TaqMan

®

48 analyzer,

COBAS

®

AMPLICOR

®

analyzer, and

cobas p 630 instrument

AMPLILINK software

Version 3.3 Series

AMPLILINK software

Roche Diagnostics

2 Application Manual · Version 1.1

Document information

Revision history

Edition notice This manual is for users of the AMPLILINK software version 3.3 series.

Some of the tests identified for use with the AMPLILINK software version 3.3 series

may not be approved for use in all countries. Contact a Roche representative for tests

that are commercially available in your country.

Every effort has been made to ensure that all the information contained in this

manual is correct at the time of printing. However, Roche Diagnostics International

Ltd reserves the right to make any changes necessary without notice as part of

ongoing product development.

Software updates are done by Roche Service representatives.

Intended use This manual is for use with AMPLILINK software version 3.3 series in conjunction

with the manuals for the COBAS

®

AmpliPrep instrument, the COBAS

®

TaqMan

®

analyzer, the COBAS

®

TaqMan

®

48 analyzer, the COBAS

®

AMPLICOR

®

analyzer, and

the cobas p 630 instrument.

Trademarks ROCHE, AMPLILINK, COBAS, COBAS P, AMPLIPREP, TAQMAN, and

AMPLICOR are trademarks of Roche.

Microsoft, Windows, and Windows XP are either registered trademarks or

trademarks of Microsoft Corporation in the United States and/or other countries.

Pentium is a registered trademark of Intel Corporation.

Contact addresses

Manual Version Software Version Revision date Changes

1.0 3.3 June 2009 Update of AMPLILINK

software 3.2 to software 3.3

1.1 3.3 April 2011 See section Changes in version

1.1 of the AMPLILINK

Application Manual on page 5

Roche Molecular Systems, Inc.

1080 US Highway 202 South

Branchburg, NJ 08876

USA

Made in Switzerland

Roche Diagnostics GmbH

Sandhofer Strasse 116

68305 Mannheim

Germany

Roche Diagnostics

Application Manual · Version 1.1 3

AMPLILINK software

Table of contents

Document information 2

Contact addresses 2

Table of contents 3

Preface 5

Changes in version 1.1 of the AMPLILINK

Application Manual 5

How to use this manual 5

Symbols and abbreviations 6

System description Part A

1 General safety information

Safety classifications A–5

Safety precautions A–6

Safety summary A–7

2 Introduction

System overview A–13

Client-server architecture A–14

Primary tube pipetting A–15

Multi-result tests A–17

About patient IDs, order numbers, and

sample IDs A–18

3 Software

Introduction to the AMPLILINK software A–23

Working with lists A–33

Working with the mouse and the keyboard A–44

Using Help A–46

Operation Part B

4Workflows

Introduction B–7

Safety information B–9

cobas p 630 instrument B–10

COBAS

®

AmpliPrep instrument -

COBAS

®

TaqMan

®

analyzer B–20

COBAS

®

AmpliPrep instrument -

COBAS

®

TaqMan

®

48 analyzer B–32

COBAS

®

AmpliPrep instrument - COBAS

®

AMPLICOR

®

analyzer B–43

COBAS

®

AmpliPrep instrument - Offline

amplification and detection B–59

Manual preparation - COBAS

®

TaqMan

®

48

analyzer B–65

Manual preparation - COBAS

®

AMPLICOR

®

analyzer B–73

Stop an instrument or analyzer during a run B–82

5 Operation

Safety information B–89

Starting up, shutting down, and restarting B–90

System handling B–92

Order handling B–99

Result handling B–136

Report handling B–153

Operator administration B–154

AMPLILINK Monitor B–156

AMPLILINK Archive Viewer B–157

Maintenance Part C

6 General maintenance

Managing service actions C–5

Troubleshooting Part D

7Flags

General flag description D–5

List of all AMPLILINK software flags D–10

COBAS

®

AMPLICOR

®

analyzer flags D–17

cobas p 630 instrument flags D–18

COBAS

®

AmpliPrep instrument flag remarks D–21

COBAS

®

TaqMan

®

analyzer and COBAS

®

TaqMan

®

48

analyzer flags with flag remark D–27

COBAS

®

TaqMan

®

analyzer and COBAS

®

TaqMan

®

48

analyzer flags without flag remark D–44

AMPLILINK software flag remarks D–54

8 General troubleshooting

Troubleshooting D–59

List of messages D–64

Roche Diagnostics

4 Application Manual · Version 1.1

AMPLILINK software

Software description Part E

9 General

Logon to the AMPLILINK software E–5

Menu description E–7

Unsupported characters E–18

10 Messages

Messages window E–21

11 Overview

Overview window E–33

12 Systems

Systems window E–43

COBAS® AmpliPrep instrument E–46

COBAS® TaqMan® analyzer E–57

COBAS® TaqMan® 48 analyzer E–63

COBAS® AMPLICOR® analyzer E–69

Run Log tab E–82

Service Due tab E–84

Service All tab E–86

Service Log tab E–88

Counters: Instrument (dialog box) E–89

Firmware Information (dialog box) E–90

13 Orders

Orders window E–93

14 Results

Results window E–119

15 Configuration

Configuration window E–135

General Configuration E–138

Maintenance Configuration E–140

Operator Access Configuration E–149

Barcode Configuration E–152

Systems configuration E–155

Lab Configuration E–157

Contacts Configuration E–165

LIS Configuration E–167

Report Layout Configuration E–184

Processing Configuration E–194

Test Definitions Configuration E–200

Export Definitions E–206

Windows configuration E–212

16 Memo Pad

Memo Pad window E–223

Glossary Part F

Glossary F–3

Index Part G

Index G–3

Revisions Part H

Revisions

Changes in AMPLILINK Software Application

Manual version 1.1 H–5

Roche Diagnostics

Application Manual · Version 1.1 5

AMPLILINK software

Preface

This manual is for use with AMPLILINK software version 3.3 series in conjunction

with the instrument manuals for the COBAS

®

AmpliPrep instrument, the COBAS

®

TaqMan

®

analyzer, the COBAS

®

TaqMan

®

48 analyzer, the COBAS

®

AMPLICOR

®

analyzer, and the cobas p 630 instrument.

Compatibility AMPLILINK software version 3.3 is compatible with the following data stations:

o Evo 510

o dc7100

o dc7600

o rp5700

The following data stations are not supported:

o VL420

o d530

Changes in version 1.1 of the AMPLILINK Application Manual

Stopping an instrument or

analyzer

The section Stop an instrument or analyzer during a run on page B-82 has been

added.

Modifying, deleting and

aborting orders

The section Modifying, deleting, and aborting orders on page B-129 has been changed

and expanded.

New flags New flags have been added in Chapter 7 Flags to cover the new calculation algorithms

on the COBAS

®

TaqMan

®

analyzer and the COBAS

®

TaqMan

®

48 analyzer.

Abort advanced The section Abort Advanced on page E-97 has been added.

General changes Minor improvements have been implemented throughout this document.

How to use this manual

To help you to find information quickly, there is a table of contents at the beginning

of the book and at the beginning of every chapter. In addition, a complete index and a

glossary of terms can be found at the end.

This manual is organized to reflect the major functions supported by the

AMPLILINK software. It contains the following chapters.

Preface Lists the conventions, symbols, and units used in the manual.

o Keep this Application Manual in a safe place to ensure that it is not damaged and

remains available for use.

o This Application Manual should be easily accessible at all times.

AMPLILINK software

Roche Diagnostics

6 Application Manual · Version 1.1

Chapter 1 General safety

information

Provides safety information.

Chapter 2 Introduction Gives an introduction to the AMPLILINK software and introduces some basic

concepts.

Chapter 3 Software Describes how to use the AMPLILINK software.

Chapter 4 Workflows Provides instructions for routine operation of the cobas p 630 instrument, COBAS

®

AmpliPrep instrument, COBAS

®

TaqMan

®

analyzer, COBAS

®

TaqMan

®

48 analyzer,

and COBAS

®

AMPLICOR

®

analyzer.

Chapter 5 Operation Provides detailed instructions on startup, and shutdown, orders handling, results

handling, and using the AMPLILINK Archive Viewer.

Chapter 6 General maintenance Provides instructions on managing service actions.

Chapter 7 Flags Explains the flags and gives recommended actions.

Chapter 8 General

troubleshooting

Describes the procedures for resolving problems during operation.

Chapters 9-16 Software

description

Describes the AMPLILINK software in detail.

Symbols and abbreviations

Visual cues are used to help locate and interpret information in this manual quickly.

This section explains formatting conventions used in this manual.

Text conventions

Symbols The following symbols are used:

Text convention Used for

Numbered lists

Numbered procedures that should be implemented sequentially

during an operation:

1

Turn power switch on.

2

Click File.

Italics

Designating another section of this manual that should be consulted.

e

For additional details, see To set up export columns on

page B-146

Bold

Terms in the user interface like tab or button names or options are

printed in bold letters.

3

Click OK to close the Custom Filter dialog box and activate the

filter.

>

Separates command options in a multi-level command:

Select File > Shut Down from the menu bar.

Roche Diagnostics

Application Manual · Version 1.1 7

AMPLILINK software

Graphics All graphics including screens and printouts are for illustration purposes only and

may deviate from your system.

Abbreviations The following abbreviations are used:

Symbol Used for

a Start of procedure

End of procedure

o List item

e

Cross-reference

Tip

Danger alert symbol

Warning alert symbol

Caution and general safety alert symbol

Electrical and electronic equipment marked with this symbol are

covered by the European directive WEEE.

The symbol denotes that the equipment must not be disposed of in

the municipal waste system.

Abbreviation Definition

BOD Begin of Day

cm Centimeters

C/mL

cp/mL

Copies per milliliter

DNA Deoxyribonucleic Acid

DP Detection Position

EOD End of Day

GZ Grey Zone

Hz Hertz

IC Internal Control

in Inches (2.54 cm)

IU/mL International Units per milliliter

kg Kilogram

lb Pounds (weight)

LAN Local Area Network

LIS Laboratory Information System

mL milliliters (10

-3

liters)

MGP Magnetic Glass Particle

NEG Negative

OD Optical Density

POS Positive

QS Quantitation Standard

AMPLILINK software

Roche Diagnostics

8 Application Manual · Version 1.1

RFI Relative Fluorescence Increase

SPU Sample Processing Unit

TC Thermal Cycler

TDF Test Definition File

TNAI Total Nucleic Acid Isolation

UPS Uninterrupted power supply

XML Extensible Markup Language

Abbreviation Definition

1 General safety information . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-3

2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-11

3 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-21

System description

A

Roche Diagnostics

Application Manual · Version 1.1 A-3

AMPLILINK software 1 General safety information

Table of contents

General safety information

This chapter provides general safety informations for working with the AMPLILINK

software. Specific safety informations are provided in the manual where required. For

specific safety informations refer also to the Instrument Manuals, the cobas p 630

instrument Operator’s Manual, and the assay-specific package inserts and Method

Manuals.

Safety classifications ........................................................................................................ A-5

Safety precautions ........................................................................................................... A-6

Operator qualification .............................................................................................. A-6

Safety summary ............................................................................................................... A-7

Warning messages .................................................................................................... A-7

Biohazardous materials ...................................................................................... A-7

Caution messages ...................................................................................................... A-8

Reagents and other working solutions ............................................................ A-8

Samples and sample racks ................................................................................. A-9

Cross contamination of samples ...................................................................... A-9

Notices ...................................................................................................................... A-10

Software virus warning .................................................................................... A-10

Third-party software ........................................................................................ A-10

Windows display settings warning ................................................................. A-10

In this chapter

Chapter

1

Roche Diagnostics

A-4 Application Manual · Version 1.1

1 General safety information AMPLILINK software

Table of contents

Roche Diagnostics

Application Manual · Version 1.1 A-5

AMPLILINK software 1 General safety information

Safety classifications

This section explains how precautionary information is presented in this manual.

The safety precautions and important user notes are classified according to the

ANSI Z535.6 Standard. Familiarize yourself with the following icons and their

meanings:

These symbols and signal words are used for specific hazards:

Important information which is not safety relevant is indicated by the following

symbol:

The safety alert symbol by itself without a signal word is used to promote awareness to

hazards which are generic or to direct the reader to safety information provided elsewhere

in the document.

DANGER

Indicates a hazardous situation which, if not avoided, will result in death or serious injury.

WARNING

Indicates a hazardous situation which, if not avoided, could result in death or serious

injury.

CAUTION

Indicates a hazardous situation which, if not avoided, could result in minor or moderate

injury.

NOTICE

Indicates a hazardous situation which, if not avoided, could result in damage to equipment.

Tip

Indicates additional information on correct use of the software, instruments, and analyzers

and gives useful tips.

Roche Diagnostics

A-6 Application Manual · Version 1.1

1 General safety information AMPLILINK software

Safety precautions

Operator qualification

Operators are required to have a sound knowledge of relevant guidelines and

standards as well as the information and procedures contained in all provided

manuals.

o Do not carry out operation and maintenance unless you have been trained by

Roche Diagnostics.

o Carefully follow the procedures specified in the provided manuals for the

operation of the software.

o Follow standard laboratory practices, especially when working with biohazardous

material.

Particular attention must be paid to the following safety precautions. If these safety

precautions are ignored, the operator may suffer serious or fatal injury. Each precaution is

important.

Roche Diagnostics

Application Manual · Version 1.1 A-7

AMPLILINK software 1 General safety information

Safety summary

This safety summary contains the most important general warning and caution

messages for working with the AMPLILINK software. Additionally, you will find

specific safety information at the beginning of Chapter

Workflows and Chapter

Operation

.

For specific safety informations refer also to the Instrument Manuals, the cobas p 630

instrument Operator’s Manual, and the assay-specific package inserts and Method

Manuals.

Warning messages

Biohazardous materials

WARNING

List of warning messages

Before operating the software, read the warning messages contained in this summary

carefully. Failure to observe them may result in death or serious injury.

Infection by samples and associated materials

Contact with samples containing material of human origin may result in infection. All

materials and mechanical components associated with samples of human origin are

potentially biohazardous.

o Follow standard laboratory practices, especially when working with biohazardous

material.

o Be sure to wear appropriate protective equipment, including, but not limited to, safety

glasses with side shields, fluid resistant lab coat, and approved disposable gloves.

o Wear a face shield if there is a chance of splash or splatter.

o If any biohazardous material is spilled, wipe it up immediately and apply disinfectant.

o If sample or waste solution comes into contact with your skin, apply immediately a

disinfectant and then wash it off with soap and water. Consult a physician.

Roche Diagnostics

A-8 Application Manual · Version 1.1

1 General safety information AMPLILINK software

Safety summary

Caution messages

Reagents and other working solutions

CAUTION

List of caution messages

Before operating the instrument, read the caution messages contained in this summary

carefully. Failure to observe them may result in minor or moderate injury.

Incorrect results due to incorrect reagent volume

Application faults may cause an undetectable loss of reagent.

o Always store reagents according to specified storage conditions.

o Reagents, once used, should not be used on other COBAS

®

AmpliPrep instruments

which are not connected to the same AMPLILINK system (a system is an AMPLILINK

client-server installation and all connected instruments and analyzers).

Incorrect results due to expired reagents or mixing kits

Data obtained using expired reagents are not reliable. Reagents are supplied in a kit

package. Mixing reagents from different kits may also lead to incorrect results.

o Do not use reagents that have exceeded their expiration dates. Replace expired

reagent with unexpired reagents before sample processing.

o Do not mix kits. Reagent cassettes from the same kit package must all be loaded

together.

Incorrect results due to reagent cassette interchange

Reagent cassettes for the COBAS

®

AmpliPrep instrument connected to the same

AMPLILINK system can be interchanged (a system is an AMPLILINK client-server

installation and all connected instruments and analyzers). But using a COBAS

®

AmpliPrep

instrument cassette already used on a COBAS

®

AmpliPrep instrument that is connected to

a different AMPLILINK system may lead to incorrect results.

Do not interchange reagents for COBAS

®

AMPLICOR

®

analyzers among different

COBAS

®

AMPLICOR

®

analyzers. Each reagent for a COBAS

®

AMPLICOR

®

analyzer may

be used on one individual COBAS

®

AMPLICOR

®

analyzer only.

A-rings can be interchanged on all COBAS

®

AMPLICOR

®

analyzers that are connected to

the same AMPLILINK system.

Roche Diagnostics

Application Manual · Version 1.1 A-9

AMPLILINK software 1 General safety information

Safety summary

Samples and sample racks

Cross contamination of samples

Incorrect results due to sample mismatch

Manual mismatch of samples or sample IDs may lead to incorrect results. Whenever

possible use a barcode scanner or an LIS for input of sample IDs to minimize manual input.

Cross-check each manual input of sample IDs to minimize manual sample mismatch.

Incorrect results due to sample rack interchange

Using a sample rack from a different AMPLILINK system may lead to incorrect results (a

system is an AMPLILINK client-server installation and all connected instruments and

analyzers).

Do not interchange sample racks among different AMPLILINK systems. Each sample rack

may be used on one individual AMPLILINK system only. Each sample rack has its own

individual rack ID, which the instrument or analyzer uses for identification purposes.

If more than one AMPLILINK system is used in the same lab, be sure to dedicate each

sample rack to one single, individual AMPLILINK system (e.g. by using individual sample

rack ID ranges for each AMPLILINK system).

Incorrect results due to carryover

Traces of analytes or reagents may be carried over from one test to the next. Take

adequate measures to safeguard additional testing and to avoid potentially false results.

Roche Diagnostics

A-10 Application Manual · Version 1.1

1 General safety information AMPLILINK software

Safety summary

Notices

Software virus warning

Third-party software

Windows display settings warning

NOTICE

List of notices

Before operating the instrument, read the notices contained in this summary carefully.

Failure to observe them may result in damage to equipment.

Data loss or unavailability of the system due to software viruses which may put

patients at risk

The data station for AMPLILINK software does not contain anti-virus protection software.

Therefore, it is essential to follow these recommendations:

o Check all diskettes, CDs, DVDs, or USB sticks with an anti-virus program (on another

PC) to ensure that they are virus free, before using them on the data station for

AMPLILINK software.

o Do not load and execute any other software on the system.

o Keep all diskettes in a secure place so that they can only be accessed by authorized

personnel.

o Use the remote services modem for contacting Roche Service or for authorized usage

only.

o Make sure other computers on the AMPLILINK software network (e.g. the LIS) are

properly secured and protected from viruses.

o Protect the AMPLILINK software network from any other network by a hardware

firewall.

o Use of cobas IT firewall is strongly recommended.

Incorrect behavior of the AMPLILINK system due to non-approved software

Installation of any third-party software that is not approved by Roche Diagnostics may

result in incorrect behavior of the AMPLILINK system. Do not install any non-approved

software.

Improper viewing of AMPLILINK software screen

The Roche field service engineer loads the AMPLILINK software and enters default

configuration settings during system installation.

Do not change the Windows display setting. Windows Classic style and Auto-hide the

taskbar must be selected for proper viewing of AMPLILINK software screens.

e

For additional details, see Display Properties (dialog box) on page E-217

Roche Diagnostics

Application Manual · Version 1.1 A-11

AMPLILINK software 2Introduction

Table of contents

Introduction

This chapter describes the new features and provides an introduction to the

AMPLILINK software.

System overview ............................................................................................................ A-13

Client-server architecture ............................................................................................ A-14

Primary tube pipetting ................................................................................................. A-15

Overview .................................................................................................................. A-15

Sample dilution ....................................................................................................... A-16

Multi-result tests ........................................................................................................... A-17

About patient IDs, order numbers, and sample IDs ................................................ A-18

In this chapter

Chapter

2

Roche Diagnostics

A-12 Application Manual · Version 1.1

2 Introduction AMPLILINK software

Table of contents

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Roche AMPLILINK 3 User manual

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