Roche cobas s 201 system User manual

Operator’s Manual

Version 1.1

For use with the

cobas® TaqScreen DPX Test

cobas® TaqScreen West Nile Virus Test

cobas® TaqScreen MPX Test

cobas® TaqScreen MPX Test, version 2.0

cobas s 201 system

Configuration E

cobas s 201 system Configuration E

Roche Diagnostics

2 Operator’s Manual · Version 1.1

Document information

Revision history

Edition notice This manual is for users of the cobas s 201 system.

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 reserves the

right to make any changes necessary without notice as part of ongoing product

development.

Any customer modification to the instrument will render the warranty or service

agreement null and void.

Software updates are performed by Roche service representatives.

Intended use The cobas s 201 system is intended for use in testing of donor specimens for

infectious agents using polymerase chain reaction (PCR) amplification technology

and 5' nuclease real-time detection technology.

The cobas s 201 system is intended to be used by laboratory professionals trained in

laboratory techniques and on the use of the system.

This manual is not to be used for applications performed using versions of the PDM

software earlier than the 4.0 series or versions of the AMPLILINK software earlier

than the 3.3 series.

Trademarks The following trademarks are acknowledged:

ROCHE, AMPERASE, AMPLILINK, AMPLIPREP, TAQMAN, TAQSCREEN,

COBAS, and COBAS S are trademarks of Roche.

HP and STORAGEWORKS are trademarks of Hewlett-Packard Company.

MICROLAB is a trademark of Hamilton Bonaduz AG.

MICROSOFT and WINDOWS are trademarks of Microsoft Corporation.

ORACLE is a trademark of Oracle Corporation.

Manual

Version Software Version Revision Date Changes

1.0 PDM software 4.0 series

AMPLILINK software 3.3

series

September 2014 Original document

1.1 PDM software 4.0 series

AMPLILINK software 3.3

series

July 2015 Caution notes regarding use of

the Abort Advanced option

were added

Roche Diagnostics

Operator’s Manual · Version 1.1 3

cobas s 201 system Configuration E

Declaration of Conformity The cobas s 201 system is comprised of the following individual components, each of

which complies with the requirements of the Directive 98/79/EC of the European

Parliament and of the Council of 27 October 1998 on In-vitro Diagnostic Medical

Devices. Compliance is provided by means of the following individual Declarations of

Conformity.

21 CFR Part 11 The Pooling and Data Management Software (PDM SW) of the cobas s 201 system is

in compliance with Title 21 CFR Part 11 of the Code of Federal Regulations. These

regulations address the FDA’s requirements on electronic records and electronic

signatures in the United States.

Contact addresses

Pooling and Data Management

(PDM)

Roche Molecular Systems, Inc.

1080 US Highway 202 South

Branchburg, NJ 08876

USA

Hamilton MICROLAB STAR IVD /

STARlet IVD pipettor

Hamilton Company

Via Crusch 8

CH-7402 Bonaduz

Switzerland

COBAS

®

AmpliPrep instrument Roche Molecular Systems, Inc.

1080 US Highway 202 South

Branchburg, NJ 08876

USA

COBAS

®

TaqMan

®

analyzer Roche Molecular Systems, Inc.

1080 US Highway 202 South

Branchburg, NJ 08876

USA

Roche Molecular Systems, Inc.

1080 US Highway 202 South

Branchburg, NJ 08876

USA

Roche Diagnostics GmbH

Sandhofer Strasse 116

68305 Mannheim

Germany

cobas s 201 system Configuration E

Roche Diagnostics

4 Operator’s Manual · Version 1.1

Roche Diagnostics

Operator’s Manual · Version 1.1 5

cobas s 201 system Configuration E

Table of contents

Document information 2

Contact addresses 3

Table of contents 5

Preface 7

Where to find information 7

How to use this manual 8

Conventions used in this manual 10

System Description Part A

1 Safety

Safety classifications A–5

Safety precautions A–6

Safety summary A–7

2 Introduction

System overview A–15

Pipetting A–17

Preparation (extraction) A–18

Amplification and detection A–19

3 Hardware and network components

Overview A–23

Laboratory information system (LIS) A–24

Firewall provided by Roche A–24

PDM server A–24

Printer A–24

Pooling and Data Management workstation A–25

Hamilton MICROLAB STAR IVD / STARlet IVD

pipettor A–26

Test m odu l e A–2 6

Checking communication A–28

4 Pooling procedures

Pipetting overview A–31

Pooling algorithm A–32

Pipetting Primary Pools of 1 A–36

Pipetting Primary Pools of 6 A–38

Pipetting Simultaneous Pools A–40

Pipetting Primary Pools of 24 A–47

Pipetting Short Run Pools of 24 A–48

Two-step pooling for Primary Pools of 96 A–49

Two-step pooling for Primary Pools of 480 A–52

DPX Library Plate pooling A–55

Pipetting Secondary Pools of 1 A–57

Pipetting Secondary Pools of 4 A–60

Pipetting Secondary Pools of 6 A–61

Pipetting Secondary Pools of 12 A–63

Pipetting Secondary Pools of 48 A–65

Flexible loading A–67

Error handling A–68

Final Pool Size A–70

Loading Capacity A–71

5 Result assignment

Overview A–87

Batch evaluation (Controls Review tab) A–90

Pool evaluation (Pools Review tab) A–90

Donor sample evaluation (Donor Review tab) A–100

6 PDM software introduction

Overview A–109

Login service A–110

Electronic signature A–113

Screen layout A–114

Sorting and sizing columns A–117

Generating reports A–118

7 Pooling Wizard

Overview A–121

Batch Run tab A–123

Plate Run tab A–128

Pipetting Progress A–130

Including UDECs in a pooling run A–132

Interrupting a pooling run A–133

Manual Pipetting tab A–135

Maintenance tab A–138

8 Pooling Manager

Overview A–141

Query tab A–143

Details tab A–147

Worklist tab A–167

AmpliLink Status tab A–171

Reports A–174

9 Data Manager

Overview A–201

Pools to review tab A–204

Batches to review tab A–210

Query tab A–212

Details tab A–217

Worklist tab A–234

Reports A–243

10 AMPLILINK software

Overview A–263

Starting up, shutting down, and restarting A–264

Organization of the work area A–268

Working with lists A–280

Messages window A–288

Overview window A–292

Systems window A–295

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6 Operator’s Manual · Version 1.1

cobas s 201 system Configuration E

Orders window A–324

Memo Pad window A–328

Operation Part B

11 Workflows

Introduction B–5

Safety information B–5

Two-step pooling for PP96 and PP480 B–6

DPX Library Plate workflow B–22

Aliquot Plate workflow B–40

One-step pooling for Primary Pools containing less

than 96 samples B–44

Manual pipetting B–58

12 Operating instructions

Safety information B–69

Workstations B–70

Hamilton MICROLAB STAR IVD / STARlet IVD

pipettor B–71

COBAS

®

AmpliPrep instrument B–74

COBAS

®

TaqMan

®

analyzer B–82

Reviewing test results B–87

Accepting and transmitting complete results B–89

Maintenance Part C

13 Service

Overview C–5

Hamilton MICROLAB STAR IVD / STARlet IVD

pipettor C–5

COBAS

®

AmpliPrep instrument C–6

COBAS

®

TaqMan

®

analyzer C–6

Troubleshooting Part D

14 Pooling run errors

Overview D–5

Loading and unloading errors D–6

Pipetting errors D–14

Workstation unresponsive D–17

15 Missing orders or results

Order download D–21

Result upload D–23

16 PDM software error messages

Overview D–29

List of PDM software messages D–30

17 AMPLILINK software error messages

Troubleshooting D–73

List of messages D–76

18 Test module flags

General flag description D–93

List of all AMPLILINK software flags D–96

COBAS

®

AmpliPrep instrument flag remarks D–100

COBAS

®

TaqMan

®

analyzer flag remarks D–105

COBAS

®

TaqMan

®

analyzer flags without a flag

remark D–116

Administrator’s guide Part E

19 PDM software administration

Pooling Manager E–5

Data Manager E–9

Configuration E–18

User Admin E–31

Report Manager E–39

20 PDM database maintenance

Archiving PDM data E–55

Archive Viewer E–59

Backing up PDM data E–73

21 AMPLILINK software administration

AMPLILINK software E–77

Glossary Part F

Glossary F–3

Index Part G

Index G–3

Revisions Part H

Revisions H–3

Roche Diagnostics

Operator’s Manual · Version 1.1 7

cobas s 201 system Configuration E

Preface

The cobas s 201 system is intended for use in testing of donor specimens for

infectious agents using polymerase chain reaction (PCR) amplification technology

and 5' nuclease real-time detection technology.

The cobas s 201 system is intended to be used by laboratory professionals trained in

laboratory techniques and on the use of the system.

This manual contains descriptions of the cobas s 201 system hardware and software

components and operational and troubleshooting procedures.

Where to find information

The following documents are available for the cobas s 201 system. Each document

contains applicable safety and troubleshooting information.

Operator’s Manual Contains a general description of the hardware and network components, pooling

procedures, and result assignment algorithms. Also contains a detailed explanation of

the software components and workflow procedures. Material in the Operator’s

Manual is customized for required assays. The contents of each chapter in the

Operator’s Manual are described starting on the next page.

Hamilton MICROLAB STAR

IVD / STARlet IVD Pipettor

Instrument Manual

Contains a detailed description of the Hamilton MICROLAB STAR IVD / STARlet

IVD pipettor, including technical specifications, pipetting operations, and hardware

components. Describes operation and maintenance procedures.

COBAS

®

AmpliPrep Instrument

Instrument Manual

Contains a detailed description of the COBAS

®

AmpliPrep instrument, including

technical specifications, sample preparation overview, and hardware components.

Describes operation and maintenance procedures.

COBAS

®

TaqMan

®

Analyzer

Instrument Manual

Contains a detailed description of the COBAS

®

TaqMan

®

analyzer, including

technical specifications, amplification and detection methodology, and hardware

components. Describes operation and maintenance procedures.

Package Inserts Contain test-specific instructions for use including specimen collection, storage, and

pooling procedures, materials required, and performance characteristics.

NOTICE

This manual is not to be used for applications performed using versions of the PDM

software earlier than the 4.0 series or versions of the AMPLILINK software earlier than the

3.3 series.

NOTICE

o Some of the tests identified for use with the cobas s 201 system may not be approved

for use in all countries. Contact a Roche representative to determine which tests are

commercially available in your country.

o Primary Pools of 24 are not available in the United States.

o Users of the cobas s 201 system tests should consult the test-specific package inserts

concerning use of the Docking Station.

cobas s 201 system Configuration E

Roche Diagnostics

8 Operator’s Manual · Version 1.1

How to use this manual

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

the book and each chapter. In addition, a complete index can be found at the end.

The cobas s 201 system Configuration E Operator’s Manual contains the following

chapters:

Preface Summarizes the conventions used in this manual.

Safety Summarizes safety precautions necessary when operating the system.

Introduction Describes the cobas s 201 system major processing steps.

Hardware and network

components

Describes the cobas s 201 system hardware and network components.

Pooling procedures Describes the general algorithm for assigning pooling methods. Contains pipetting

diagrams to show pipetting patterns for each method.

Result assignment Explains how PDM software assigns batch, pool, and donor sample results.

PDM software introduction Provides a description of all PDM software components and describes common

functions.

Pooling Wizard Describes the Pooling Wizard software, which is used to operate the Hamilton

MICROLAB STAR IVD / STARlet IVD pipettor.

Pooling Manager Describes the Pooling Manager software, which is used to review pooling run status.

Data Manager Describes the Data Manager software, which is used to review and accept results, and

to transmit accepted results to the LIS.

AMPLILINK software Describes the AMPLILINK software, which is used to operate the COBAS

®

AmpliPrep instrument and COBAS

®

TaqMan

®

analyzer.

Workflows Contains instructions for routine operation of the cobas s 201 system.

Operating instructions Provides detailed instructions for starting up and loading the instruments and

reviewing, accepting, and transmitting results to the LIS.

Service Summarizes steps required for regular service of the cobas s 201 system hardware

components.

Pooling run errors Lists errors that may occur during a pooling run and provides recommended actions

for resolving the problems.

Missing orders or results Describes problems that may occur downloading orders and uploading results.

Contains instructions for determining order and result status and retransmitting

missing data.

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

remains available for use.

o This Operator’s Manual must be easily accessible at all times.

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Operator’s Manual · Version 1.1 9

cobas s 201 system Configuration E

PDM software error messages Lists all PDM software error messages and provides recommended actions.

AMPLILINK software error

messages

Lists all AMPLILINK software error messages and provides recommended actions.

Test module flags Lists all flags that can be generated by the COBAS

®

AmpliPrep instrument or

COBAS

®

TaqMan

®

analyzer and provides causes and recommended actions.

PDM software administration Describes the PDM software functions accessible to the laboratory administrator.

PDM database maintenance Explains how to archive and backup the PDM database.

AMPLILINK software

administration

Describes the AMPLILINK software functions accessible to the laboratory

administrator.

Glossary Contains definitions for specialized terms used in this manual.

Index Provides a list of reference pages for key terms in this manual.

cobas s 201 system Configuration E

Roche Diagnostics

10 Operator’s Manual · Version 1.1

Conventions used in this manual

This section explains the formatting conventions used in this manual.

Text conventions To convey information readily and consistently, certain text conventions are used

throughout this manual. These text conventions are as follows:

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

This section explains formatting conventions used in this manual.

Symbols The following symbols are used:

Text Convention Used for

Numbered lists

Numbered procedures to be implemented sequentially during an

operation:

1. Display the Donor Review tab.

2. Select the required status filter.

Italics

Designating another section of this manual to be consulted.

e

For details, see Symbols on page 10

Bold

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

printed in bold letters.

1. Select the Pooling Wizard Maintenance tab.

2. Select Weekly Maintenance, then click Start.

>

Separates command options in a multi-level command:

Choose File > Shut Down from the menu bar.

Symbol Used for

a Start of procedure

End of procedure

o List item

e

Cross-reference

f Call-up (software 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.

Global Trade Item Number. Used on the type plate of the instrument.

Roche Diagnostics

Operator’s Manual · Version 1.1 11

cobas s 201 system Configuration E

Screenshots The screen representations shown in this publication are for illustrative purposes

only. The screens do not necessarily show valid data.

Abbreviations The following abbreviations are used.

µL Microliters (10

-6

liters)

AFI Absolute fluorescent increase

ALR Above linear range

ASTM American Society for Testing and Materials

B19 Parvovirus B19

BOD Beginning-of-day

BSCU Blood screening control unit

BSL-2 Biosafety level 2

CAC Cycle number of annealing temperature change

CAN Canada

CAP COBAS

®

AmpliPrep instrument

CFR Code of Federal Regulations (USA)

cLLD Capacitive liquid level detection

CLSI Clinical Laboratory Standards Institute

cm Centimeters

CO-RE Compression-induced O-ring expansion

CPU Central processing unit

CSA Canadian Standards Association

CSV Comma-separated values

Ct Cycle threshold

CTM COBAS

®

TaqMan

®

analyzer

CTS Clinical trial support

DNA Deoxyribonucleic acid

DPC Duplex positive control (positive qualitative control for HAV

and low positive quantitative control for B19)

DPX Duplex

DPX test cobas ® TaqScreen DPX Test

DSLM Double sigmoid Levenberg-Marquardt (equation)

DVD Digital versatile disc

EC European community

EN European normative

EOD End-of-day

FCC Federal Communications Commission

FTP File transfer protocol

GB Gigabyte

GHz Gigahertz

HAV Hepatitis A Virus

HBV Hepatitis B Virus

HCV Hepatitis C Virus

HIV Human immunodeficiency Virus

Hz Hertz

cobas s 201 system Configuration E

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12 Operator’s Manual · Version 1.1

IC Internal control

IEC International Electrotechnical Commission

in Inches

IP Intermediate Plate

IU International units

kg Kilogram

LAN Local area network

lb Pounds (weight)

LED Light emitting diode

LIS Laboratory information system

LLD Liquid level detection

LMOM Levenberg-Marquardt outlier method

LP Library Plate

MB Megabytes (10

6

bytes)

MGP Magnetic glass particles

mL Milliliters (10

-3

liters)

mm Millimeter (10

-3

meters)

MMx Master Mix

MPC Multiplex positive control (positive qualitative control for

HIV-1 M, HBV, HCV)

MPX Multiplex (also appears on some screens as an abbreviation

for cobas® TaqScreen MPX Test)

MPX test cobas® TaqScreen MPX Test

MPX v2.0 test cobas® TaqScreen MPX Test, version 2.0

MPX2 Appears on some screens as an abbreviation for

cobas® TaqScreen MPX Test, version 2.0

ms Milliseconds

NEG Negative

OD Optical density

PCR Polymerase chain reaction

PDF Portable document format

PDM Pooling and data management

pipettor Hamilton MICROLAB STAR IVD / STARlet IVD pipettor

PlateIP Intermediate Plate Run for the DPX LP workflow

PlateLP Library Plate Run

Platen Batch Run for the DPX LP workflow

pLLD Pressure LLD

POS Positive

PPn Primary Pools of n

QS Quantitation standard

RAM Random-access memory

ResP1 Resolution Pooling

RF Radio frequency

RFI Relative fluorescence increase

RMEC Roche-manufactured external control

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Operator’s Manual · Version 1.1 13

cobas s 201 system Configuration E

,

rPPn Repeat Primary Pools of n

rResP1 Repeat Resolution Pooling

rSPn Repeat Secondary Pools of n

RT Reverse transcription

R-tip Reagent tip

RW Read write

S/N Serial number

SPn Secondary Pools of n

SPU Sample processing unit

STAR Hamilton MICROLAB STAR IVD pipettor (in certain cases,

Hamilton MICROLAB STARlet IVD pipettor)

STARlet Hamilton MICROLAB STARlet IVD pipettor

StepMOM Internal step correction algorithm

S-tip Sample tip

TC Thermal cycler

TDF Test definition file

TND Target not detected

TS TaqScreen

UDEC User-defined external control

UL Underwriters Laboratories Inc.

UPS Uninterruptible power supply

US United States

USB Universal serial bus

UV Ultraviolet

VVolt

VA Volt-Ampères (power consumption)

VAC Volts (alternating current)

WWatt

WEEE Waste from electric and electronic equipment

WNV West Nile Virus

WNV test cobas ® TaqScreen West Nile Virus Test

cobas s 201 system Configuration E

Roche Diagnostics

14 Operator’s Manual · Version 1.1

1 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–3

2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–13

3 Hardware and network components . . . . . . . . . . . . . . . . . . . . . A–21

4 Pooling procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–29

5 Result assignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–85

6 PDM software introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . A–107

7 Pooling Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–119

8 Pooling Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–139

9 Data Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–199

10 AMPLILINK software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–261

System Description

A

Roche Diagnostics

Operator’s Manual · Version 1.1 A-3

cobas s 201 system Configuration E 1 Safety

Tabl e of con tents

Safety

This chapter provides general safety information for working with the cobas s 201

system. Specific safety instructions are provided in the manual where required. For a

description of safety labels on the instruments and instructions for disposal of the

instruments, refer to the specific Instrument Manuals. For additional safety

information refer to the test-specific package inserts.

Safety classifications ................................................................................................... A–5

Safety precautions ...................................................................................................... A–6

Operator qualification .......................................................................................... A–6

Safe and proper use of the instruments ............................................................... A–6

Safety summary .......................................................................................................... A–7

Warning messages ................................................................................................ A–7

Biohazardous materials .................................................................................. A–7

Optical safety .................................................................................................. A–7

Caution messages ................................................................................................. A–8

Mechanical safety ........................................................................................... A–8

Proper sample identification .......................................................................... A–8

Correct use of pipette tips .............................................................................. A–9

Proper sample and control loading ............................................................... A–9

Reagents and other working solutions .......................................................... A–9

Cross contamination of samples .................................................................. A–10

Notices ................................................................................................................ A–11

Moving parts ................................................................................................. A–11

Proper operation .......................................................................................... A–11

Proper loading .............................................................................................. A–11

Third-party software .................................................................................... A–11

Windows display settings ............................................................................. A–11

Software viruses ............................................................................................ A–12

In this chapter

Chapter

1

Roche Diagnostics

A-4 Operator’s Manual · Version 1.1

1 Safety cobas s 201 system Configuration E

Tabl e of con tents

Roche Diagnostics

Operator’s Manual · Version 1.1 A-5

cobas s 201 system Configuration E 1 Safety

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 that 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 that 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, can result in death or serious injury.

CAUTION

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

injury.

NOTICE

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

Tip

Indicates additional information on correct use of the instrument or useful tips.

Roche Diagnostics

A-6 Operator’s Manual · Version 1.1

1 Safety cobas s 201 system Configuration E

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 the Operator’s

Manual and Instrument Manuals.

o Do not perform operation and maintenance unless you have been trained.

o Carefully follow the procedures specified in the Operator’s Manual and

Instrument Manuals for the operation and maintenance of the instruments.

o Leave maintenance, installation, or service that is not described in the Operator’s

Manuals to trained Roche Service personnel.

o Follow standard laboratory practices, especially when working with biohazardous

material.

Safe and proper use of the instruments

Personal protective equipment 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.

Accuracy/precision of measured

results

o Each laboratory must verify that instrument and reagent performance meets the

published specifications.

Correct use o Use the system only for preparing liquid samples with the provided reagents as

defined in the test-specific package insert.

Operating conditions o Operation outside of the specified ranges may lead to incorrect results or

malfunction of the instruments (see technical specifications in the Instrument

Manuals).

o Keep the Operator’s Manual in a safe place to ensure that it is not damaged and

remains available for use. This manual must be easily accessible at all times.

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.

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