Roche AMPLILINK 3 User manual

AMPLILINK Software

Application Manual

Version 1.0

Software Version 3.4 Series

AMPLILINK Software

Software Version 3.4 Series

Roche Diagnostics

2 Application Manual · Version 1.0

Publication information

Edition notice This publication is intended for operators of the AMPLILINK Software Version 3.4

Series.

Some of the tests identified for use with the AMPLILINK Software Version 3.4 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 publishing. However, Roche Molecular Systems, Inc.

may need to update the manual information as output of product surveillance

activities, leading to a new version of this manual.

CAUTION

General attention

To avoid incorrect results, ensure that you are familiar with the instructions and safety

information.

r Pay particular attention to all safety notices.

r Always follow the instructions in this publication.

r Do not use the software in a way that is not described in this publication.

r Store all publications in a safe and easily retrievable place.

Training Do not carry out operation tasks or maintenance actions unless you have received

training from Roche Diagnostics. Leave tasks that are not described in the user

documentation to trained Roche Service representatives.

Screenshots The screenshots in this publication have been added exclusively for illustration

purposes. Configurable and variable data, such as tests, results, or path names visible

therein must not be used for laboratory purposes.

Warranty Any customer modification to the system renders the warranty or service agreement

null and void.

For conditions of warranty, contact your local sales representative or refer to your

warranty contract partner.

Always leave software updates to a Roche Service representative or perform such

updates with their assistance.

Trademarks The following trademarks are acknowledged:

AMPLILINK, COBAS, COBAS P, AMPLIPREP, and TAQMAN are trademarks of

Roche.

All other trademarks are the property of their respective owners.

Publication

version

Software version Revision date Change description

1.0 3.4 June 2015 This is the first version of the AMPLILINK Software Version 3.4

Series Application Manual. The changes in the Application

Manual reflect the update from Software Version 3.3 Series to

Software Version 3.4 Series.

Table 1 Revision history

Roche Diagnostics

Application Manual · Version 1.0 3

AMPLILINK Software

Software Version 3.4 Series

Open source license notification

and licenses

The AMPLILINK Software might contain components or modules that are open

source or commercial software programs. For copyright, other notices, and licensing

information regarding such software programs included with the AMPLILINK

Software please see the CD/DVD provided with the product or the folder “Licensing

Information” located on the hard disk drive D of the AMPLILINK control unit.

Feedback Every effort has been made to ensure that this publication fulfills the intended use. All

feedback on any aspect of this publication is welcome and is considered during

updates. Contact your Roche representative, should you have any such feedback.

Approvals The AMPLILINK Software meets the requirements of the Directive 98/79/EC.

Contact addresses

Complies with the IVD directive 98/79/EC.

For in vitro diagnostic use.

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

AMPLILINK Software

Software Version 3.4 Series

Roche Diagnostics

4 Application Manual · Version 1.0

Roche Diagnostics

Application Manual · Version 1.0 5

AMPLILINK Software

Software Version 3.4 Series

Table of contents

Publication information 2

Contact addresses 3

Table of contents 5

Intended use 7

Compatibility 7

How to use this publication 7

Symbols and abbreviations 8

What is new in version 1.0 of the publication

for AMPLILINK Software version 3.4 10

System description

1 General safety information

Safety classifications 17

Safety precautions 18

Safety summary 19

2 Introduction

System overview 25

Client-server architecture 26

Primary tube pipetting 27

Multi-result tests 29

About patient IDs, order numbers, and

sample IDs 30

3 Software

Introduction to the AMPLILINK Software 35

Working with lists 45

Working with the mouse and the keyboard 55

Using Help 57

Operation

4 Workflows

Introduction 69

Safety information 71

cobas p 630 instrument 72

COBAS

®

AmpliPrep Instrument -

COBAS

®

TaqMan

®

Analyzer 80

COBAS

®

AmpliPrep Instrument -

COBAS

®

TaqMan

®

48 Analyzer 90

COBAS

®

AmpliPrep Instrument - Offline

amplification and detection 100

Manual preparation - COBAS

®

TaqMan

®

48

Analyzer 106

Stop an instrument or analyzer during a run 113

5 Operation

Safety information 119

Starting up, shutting down, and restarting 120

System handling 123

Order handling 125

Result handling 153

Report handling 167

Operator administration 168

AMPLILINK Monitor 170

AMPLILINK Archive Viewer 172

Maintenance

6 General maintenance

Managing service actions 183

Troubleshooting

7 Flags

General flag description 191

List of all AMPLILINK Software flags 196

cobas p 630 instrument flags 200

COBAS

®

AmpliPrep Instrument flag remarks 203

COBAS

®

TaqMan

®

Analyzer and

COBAS

®

TaqMan

®

48 Analyzer flags with flag

remark 210

COBAS

®

TaqMan

®

Analyzer and

COBAS

®

TaqMan

®

48 Analyzer flags without

flag remark 224

AMPLILINK Software flag remarks 235

8 General troubleshooting

Troubleshooting 239

List of messages 244

Software description

9 General

Logon to the AMPLILINK Software 263

Menu description 265

AMPLILINK Information (dialog box) 274

Unsupported characters 275

10 Messages

Messages window 279

Tasks in Messages window 285

11 Overview

Overview window 289

Tasks in Overview window 296

Roche Diagnostics

6 Application Manual · Version 1.0

AMPLILINK Software

Software Version 3.4 Series

12 Systems

Systems window 299

COBAS

®

AmpliPrep Instrument 301

COBAS

®

TaqMan

®

Analyzer 310

COBAS

®

TaqMan

®

48 Analyzer 315

Run Log tab 320

Service Due tab 322

Service All tab 324

Service Log tab 326

Counters: Instrument (dialog box) 327

Firmware Information (dialog box) 328

Tasks in Systems window 329

13 Orders

Orders window 335

Order origin 350

Order status 351

Rack order status 352

Sample status 353

Test type 354

14 Results

Results window 357

15 Configuration

Configuration window 373

General Configuration 376

Maintenance Configuration 378

Operator Access Configuration 387

Barcode Configuration 391

Systems configuration 393

Lab Configuration 395

Contacts Configuration 400

LIS Configuration 402

Report Layout Configuration 412

Processing Configuration 420

Test Definitions Configuration 424

Export Definitions 428

Windows configuration 434

Tasks in Configuration window 442

16 Memo Pad

Memo Pad window 455

Glossary

17 Glossary

Index

Index 465

Revisions

Roche Diagnostics

Application Manual · Version 1.0 7

AMPLILINK Software

Software Version 3.4 Series

Intended use

As a component of the COBAS

®

AmpliPrep Instrument/COBAS

®

TaqMan

®

Analyzer

2

nd

generation system, the AMPLILINK Software is used to integrate all instruments

and analyzers offering a single user interface for PCR testing. AMPLILINK Software

supports various instrument configurations, data management, and analysis of test

results from clinical specimens using PCR technology.

Test results can be automatically transferred to an external host.

The AMPLILINK Software is setup as a client/server architecture. This allows the use

of several decentralized AMPLILINK control units each controlling individual

instruments and/or analyzers.

The AMPLILINK Software also handles the test definition file (TDF) for each assay it

supports, captures sample identification, absorbance results, and interpretations and

comments from the data output for the instruments it supports and presents the data

in the user interface.

Compatibility

AMPLILINK Software Software Version 3.4 Series is compatible with the following

control units:

o rp5700

o rp5800

The following control units are not supported:

o VL420

o d530

o Evo 510

o dc7100

o dc7600

How to use this publication

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.

Chapter 1 General safety

information

Provides safety information.

u Chapter General safety information

AMPLILINK Software

Software Version 3.4 Series

Roche Diagnostics

8 Application Manual · Version 1.0

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

concepts.

u Chapter Introduction

Chapter 3 Software Describes how to use the AMPLILINK Software.

u Chapter Software

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

COBAS

®

AmpliPrep Instrument, COBAS

®

TaqMan

®

Analyzer, and

COBAS

®

TaqMan

®

48 Analyzer.

u Chapter Workflows

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

handling, and using the AMPLILINK Archive Viewer.

u Chapter Operation

Chapter 6 General maintenance Provides instructions on managing service actions.

u Chapter General maintenance

Chapter 7 Flags Explains the flags and gives recommended actions.

u Chapter Flags

Chapter 8 General troubleshooting Describes the procedures for resolving problems during operation.

u Chapter General troubleshooting

Chapters 9-16 Software

description

Describes the AMPLILINK Software in detail.

u Chapter General

Chapter Messages

Chapter Overview

Chapter Systems

Chapter Orders

Chapter Results

Chapter Configuration

Chapter Memo Pad

Symbols and abbreviations

Symbols used in the publication

Symbol Explanation

p Start of procedure

s End of procedure

o List item

u Cross-reference

q Tip

Danger alert symbol

Table 2 Symbols used in the publication

Roche Diagnostics

Application Manual · Version 1.0 9

AMPLILINK Software

Software Version 3.4 Series

Abbreviations The following abbreviations are used:

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.

Symbol Explanation

Table 2 Symbols used in the publication

Abbreviation Definition

AFI Absolute Fluorescence Increase

BLS Baseline Subtraction Elbow (algorithm)

BOD Begin of Day

cm Centimeters

C/mL

cp/mL

Copies per milliliter

DNA Deoxyribonucleic Acid

DP Detection Position

DSLM Double Sigmoid Levenberg Marquardt (flag group)

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

RFI Relative Fluorescence Increase

SPU Sample Processing Unit

TC Thermal Cycler

TDF Test Definition File

Table 3 Abbreviations

AMPLILINK Software

Software Version 3.4 Series

Roche Diagnostics

10 Application Manual · Version 1.0

What is new in version 1.0 of the publication for AMPLILINK

Software version 3.4

Changes in the front matter and

preface

Front matter and preface have been updated according to the new Roche Diagnostics

standards.

General safety information o Section Software and data security was updated to reflect the latest Roche

Diagnostics standards.

u For details, see Software and data security (p. 21)

o Firewall recommendation (FortiGate-40C firewall) added.

u For details, see Software and data security (p. 21)

Control unit o Compatibility list for control units updated.

u For details, see Compatibility (p. 7)

o Term "data station" changed to "control unit".

Data encryption and data

masking

Information about data encryption and data masking added.

u For details, see Data encryption and data masking (p. 26)

Barcode clips Notes about the proper insertion of the barcode clips into the sample rack positions

have been added. A clicking sound indicates that the barcode clip snaps into place.

Startup procedure Further details about the start up procedure have been added.

u For details, see Perform start up procedures (p. 81) and Starting up, shutting down, and

restarting (p. 120)

Patient first and last name It is not possible to enter more than 30 characters for the patient’s last and first name.

Sample ID The length of the sample ID is limited to 20 characters.

Result upload Only reviewed results (results that are either accepted or rejected) can be uploaded to

the LIS. It is not possible to upload results before the Operator has reviewed them.

The Result Upload dialog box was restructured and has new options about partial

result upload for CT, RFI, and AFI values for COBAS

®

TaqMan

®

Analyzer and

COBAS

®

TaqMan

®

48 Analyzer results.

u For details, see Result Upload tab (p. 404)

TNAI Total Nucleic Acid Isolation

UPS Uninterrupted power supply

XML Extensible Markup Language

Abbreviation Definition

Table 3 Abbreviations

Roche Diagnostics

Application Manual · Version 1.0 11

AMPLILINK Software

Software Version 3.4 Series

General changes in the document o Any reference to the COBAS® AMPLICOR® analyzer removed.

o Any reference to the sample preparation methods (Generic and Probe) removed.

o The Microsoft Windows operating system version is no longer specified.

o Screenshots updated where necessary.

o Any reference to cobas Link (TeleService-Net) removed.

AMPLILINK Software

Software Version 3.4 Series

Roche Diagnostics

12 Application Manual · Version 1.0

System description

1 General safety information.............................................................................................................. 15

2 Introduction...................................................................................................................................... 23

3 Software............................................................................................................................................ 33

Roche Diagnostics

Application Manual · Version 1.0 15

AMPLILINK Software 1 General safety information

Table of contents Software Version 3.4 Series

General safety information 1

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 for

COBAS

®

AmpliPrep Instrument, COBAS

®

TaqMan

®

Analyzer, and

COBAS

®

TaqMan

®

48 Analyzer, the cobas p 630 instrument Operator’s Manual, and

the assay-specific package inserts and Method Manuals.

In this chapter

Chapter

1

Safety classifications.............................................................................................................17

Safety precautions.................................................................................................................18

Operator qualification...................................................................................................18

Safety summary ....................................................................................................................19

Warning messages..........................................................................................................19

Biohazardous materials ...........................................................................................19

Caution messages...........................................................................................................19

Reagents and other working solutions ..................................................................20

Samples and sample racks.......................................................................................20

Cross contamination of samples ............................................................................20

Notices .............................................................................................................................21

Software and data security......................................................................................21

Windows display settings warning ........................................................................22

Roche Diagnostics

16 Application Manual · Version 1.0

1 General safety information AMPLILINK Software

Table of contents Software Version 3.4 Series

Roche Diagnostics

Application Manual · Version 1.0 17

AMPLILINK Software 1 General safety information

Software Version 3.4 Series Safety classifications

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:

Generic safety precaution

r 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.

These symbols and signal words are used for specific hazards:

WARNING

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

injury.

CAUTION

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

injury.

NOTICE

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

equipment.

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

symbol:

q

Tip

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

and gives useful tips.

Roche Diagnostics

18 Application Manual · Version 1.0

1 General safety information AMPLILINK Software

Safety precautions Software Version 3.4 Series

Safety precautions

Generic safety precaution

r 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.

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.

Roche Diagnostics

Application Manual · Version 1.0 19

AMPLILINK Software 1 General safety information

Software Version 3.4 Series Safety summary

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 for

COBAS

®

AmpliPrep Instrument, COBAS

®

TaqMan

®

Analyzer, and

COBAS

®

TaqMan

®

48 Analyzer, the cobas p 630 instrument Operator’s Manual, and

the assay-specific package inserts and Method Manuals.

Warning messages

WARNING

List of warning messages

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

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

Biohazardous materials

WARNING

Infection by samples and associated materials

r 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.

Caution messages

CAUTION

List of caution messages

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

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

Roche Diagnostics

20 Application Manual · Version 1.0

1 General safety information AMPLILINK Software

Safety summary Software Version 3.4 Series

Reagents and other working solutions

WARNING

Incorrect results due to incorrect reagent volume

r 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).

WARNING

Incorrect results due to expired reagents or mixing kits

r 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.

WARNING

Incorrect results due to reagent cassette interchange

r 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.

Samples and sample racks

WARNING

Incorrect results due to sample mismatch

r 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.

WARNING

Incorrect results due to sample rack interchange

r 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).

Cross contamination of samples

WARNING

Incorrect results due to carryover

r 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.

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Roche AMPLILINK 3 User manual

Roche AMPLILINK 3 User manual

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