Roche cobas s 201 system User manual

Operator’s Manual

Version 2.0

For use with the

cobas® TaqScreen DPX Test

cobas® TaqScreen West Nile Virus Test

cobas® TaqScreen MPX Test, version 2.0

cobas s 201 system

Configuration E

Roche Diagnostics

Operator’s Manual · Version 2.0 3

cobas s 201 system Configuration E

Publication information

Revision history

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

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

publication is correct at the time of publishing. However, the manufacturer of this

product may need to update the publication information as output of product

surveillance activities, leading to a new version of this publication.

Where to find information The following documents are available for the cobas s 201 system. Each document

contains applicable safety and troubleshooting information.

The Operator’s Manual contains a general description of the hardware and network

components, pooling procedures, and result assignment algorithms. It 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.

The 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. It describes operation and maintenance procedures.

The COBAS

®

AmpliPrep Instrument Instrument Manual contains a detailed

description of the COBAS

®

AmpliPrep Instrumentt, including technical

specifications, sample preparation overview, and hardware components. It describes

operation and maintenance procedures.

The COBAS

®

TaqMan

®

Analyzer Instrument Manual contains a detailed description

of the COBAS

®

TaqMan

®

Analyzer, including technical specifications, amplification

and detection methodology, and hardware components. It 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.

Publication

version

Software version Revision date Change description

1.0 PDM software 4.0 series

AMPLILINK Software 3.3

September 2014 Original document

1.1 PDM software 4.0 series

AMPLILINK Software 3.3

July 2015 Caution notes regarding use of the Abort Advanced

option were added

2.0 PDM software 4.1 series

AMPLILINK Software 3.4 series

January 2019

e

What is new in publication version 2.0 on page 13

cobas s 201 system Configuration E

Roche Diagnostics

4 Operator’s Manual · Version 2.0

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.

Images The screenshots and hardware images in this publication have been added exclusively

for illustration purposes. Configurable and variable data in screenshots, 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.

Software updates are performed by Roche service representatives.

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

updates with their assistance.

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.

All other trademarks are the property of their respective owners.

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.

General attention

To avoid serious or fatal injury, ensure that you are familiar with the system and safety

information before you use the system.

o Pay particular attention to all safety precautions.

o Always follow the instructions in this publication.

o Do not use the instrument in a way that is not described in this publication.

o Store all publications in a safe and easily accessible place.

Roche Diagnostics

Operator’s Manual · Version 2.0 5

cobas s 201 system Configuration E

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

which meets the requirements laid down in:

Directive 98/79/EC of the European Parliament and of the Council of 27 October

1998 on in vitro diagnostic medical devices.

Directive 2011/65/EU of the European Parliament and of the Council of 8 June 2011

on the restriction of the use of certain hazardous substances in electrical and

electronic equipment.

Compliance with the applicable directive(s) is provided by means of the following

individual Declarations of Conformity.

The following marks demonstrate compliance:

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

For in vitro diagnostic use.

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

6 Operator’s Manual · Version 2.0

Roche Diagnostics

Operator’s Manual · Version 2.0 7

cobas s 201 system Configuration E

Table of contents

Publication information 3

Contact addresses 5

Table of contents 7

Intended use 9

Symbols and abbreviations 10

What is new in publication version 2.0 13

System Description Part A

1Safety

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 module A–26

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

Pipetting Secondary Pools of 1 A–55

Pipetting Secondary Pools of 4 A–58

Pipetting Secondary Pools of 6 A–59

Pipetting Secondary Pools of 12 A–61

Pipetting Secondary Pools of 48 A–63

Flexible loading A–65

Error handling A–66

Final Pool Size A–67

Loading Capacity A–68

5 Result assignment

Overview A–79

Batch evaluation (Controls Review tab) A–82

Pool evaluation (Pools Review tab) A–82

Donor sample evaluation (Donor Review tab) A–91

6 PDM software introduction

Overview A–99

Login service A–100

Electronic signature A–103

Screen layout A–104

Sorting and sizing columns A–107

Generating reports A–108

7 Pooling Wizard

Overview A–111

Batch Run tab A–113

Plate Run tab A–118

Pipetting Progress A–120

Including UDECs in a pooling run A–122

Interrupting a pooling run A–123

Manual Pipetting tab A–125

Maintenance tab A–128

8 Pooling Manager

Overview A–131

Query tab A–133

Details tab A–137

Work list tab A–158

AmpliLink Status tab A–163

Reports A–166

9 Data Manager

Overview A–177

Pools to review tab A–180

Batches to review tab A–186

Query tab A–188

Details tab A–193

Work list tab A–210

Reports A–219

10 AMPLILINK Software

Overview A–227

Starting up, shutting down, and restarting A–228

Organization of the work area A–232

Working with lists A–244

Messages window A–252

Overview window A–256

Systems window A–259

Orders window A–288

Memo Pad window A–292

Roche Diagnostics

8 Operator’s Manual · Version 2.0

cobas s 201 system Configuration E

Operation Part B

11 Workflows

Introduction B–5

Safety information B–5

Two-step pooling for PP96 and PP480 B–6

Aliquot Plate workflow B–22

One-step pooling for Primary Pools containing less

than 96 samples B–26

Manual pipetting B–40

12 Operating instructions

Safety information B–51

Workstations B–52

Hamilton MICROLAB STAR IVD / STARlet IVD

pipettor B–53

COBAS

®

AmpliPrep Instrument B–56

COBAS

®

TaqMan

®

Analyzer B–64

Reviewing test results B–69

Accepting and transmitting complete results B–71

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–12

Workstation unresponsive D–15

15 Missing orders or results

Order download D–19

Result upload D–22

16 PDM software error messages

Overview D–27

List of PDM software messages D–28

17 AMPLILINK Software error messages

Troubleshooting D–71

List of messages D–74

18 Test module flags

General flag description D–91

List of all AMPLILINK Software flags D–94

COBAS

®

AmpliPrep Instrument flag remarks D–98

COBAS

®

TaqMan

®

Analyzer flag remarks D–103

COBAS

®

TaqMan

®

Analyzer flags without a flag

remark D–114

Administrator’s guide Part E

19 PDM software administration

Pooling Manager E–5

Data Manager E–9

Configuration E–19

User Admin E–32

Report Manager E–40

20 PDM database maintenance

Archiving PDM data E–57

Archive Viewer E–60

Backing up PDM data E–76

21 AMPLILINK Software administration

AMPLILINK Software E–79

Glossary Part F

Glossary F–3

Index Part G

Index G–3

Revisions Part H

Roche Diagnostics

Operator’s Manual · Version 2.0 9

cobas s 201 system Configuration E

Intended use

The AMPLILINK Software 3.4 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.

NOTICE

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

software earlier than the 4.1 series or versions of the AMPLILINK Software earlier than the

3.4.

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 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

10 Operator’s Manual · Version 2.0

Symbols and abbreviations

Symbols used in the publication

Symbols used on product

Abbreviations The following abbreviations are used.

Symbol Explanation

a Start of procedure

End of procedure

o List item

e

Cross-reference

f Call-up (software reference)

Tip

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

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

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

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

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

Roche Diagnostics

Operator’s Manual · Version 2.0 11

cobas s 201 system Configuration E

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

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

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

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

cobas s 201 system Configuration E

Roche Diagnostics

12 Operator’s Manual · Version 2.0

PlateLP Library Plate Run

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

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

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

Roche Diagnostics

Operator’s Manual · Version 2.0 13

cobas s 201 system Configuration E

What is new in publication version 2.0

General changes o The publication was updated to PDM software version 4.1 and to AMPLILINK

Software

version 3.4.

o The term “data station” was replaced with “control unit”.

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

standards:

o The following sections were added:

e

Training on page 4

e

Images on page 4

e

Feedback on page 4

e

Symbols used on product on page 10

o The following sections were updated:

e

Edition notice on page 3

e

Where to find information on page 3

e

War rant y on page 4

e

Trademarks on page 4

e

Symbols used in the publication on page 10

o The approvals were updated and expanded:

e

Approvals on page 5

o The company name in the copyright information was adapted:

e

Copyright on page 4

o The sections How to use this manual and Text conve ntions were removed.

Safety The Danger classification was removed:

e

Safety classifications on page A-5

Windows operating system The publication was updated to reflect the current hardware and the update in the

Windows operating system.

e

Software viruses on page A-12

e

Overview on page A-23

e

Login service on page A-100

e

Start up procedures on page B-52

e

Saving reports in PDF format on page E-51

e

Examining archive data on page E-59

MPX tests The cobas® TaqScreen MPX Test was removed.

e

MPX v2.0 test on page A-71

e

Target result on page A-80

e

MPX v2.0 test on page A-84

e

MPX v2.0 test on page A-92

e

Determining RMEC requirements on page B-55

e

Channel number (optional) on page D-92

cobas s 201 system Configuration E

Roche Diagnostics

14 Operator’s Manual · Version 2.0

Restart of workstation The Pooling and Data Management workstation should be restarted at the start of the

first work day each week.

e

Pooling and Data Management workstation on page A-25

Checking communication Information was added about the display of multiple database icons.

e

Checking communication on page A-28

Error handling The behavior of the system in case of pipetting errors was updated.

e

Batch Run for Primary Pools containing < 96 samples on page A-66

Login service The procedure to log off and the procedure to switch off or restart a workstation were

updated.

e

To log off on page A-101

e

To switch off or restart a workstation on page A-101

Visibility of notifications New notifications are only displayed if a LABADMIN user is logged in. Unconfirmed

notifications are visible to LABUSER level.

e

Notification of alarms on page A-102

Display of random text Information was added about a possible window with random text.

e

Carrier/Rack Information panel on page A-116

e

Determining consumable requirements on page B-54

RMEC icons The color-coding of RMEC icons was updated.

e

Color coding of icons on page A-120

Results The SK24 rack must be removed from the COBAS

®

TaqMan

®

Analyzer for results to

be sent to PDM.

e

Overview on page A-227

e

Review results on page B-18

e

Review results on page B-35

e

Review results on page B-46

e

Result upload on page D-22

Repeated characters AMPLILINK Software passwords cannot contain repeated characters.

e

Changing your password on page A-231

e

Operator access configuration on page E-92

Obtaining donor samples The information for the maximum and minimum number of donor samples was

updated.

e

Obtain donor samples on page B-7

Storing samples The visual check for consistent volume was removed.

e

Store samples on page B-9

Manual pipetting Up to 24 S-tubes can be included in a manual pipetting run.

e

Manual pipetting on page B-40

Roche Diagnostics

Operator’s Manual · Version 2.0 15

cobas s 201 system Configuration E

Carrier identification errors The system behavior in case of carrier identification errors was updated. The

procedure how to enter a carrier barcode manually was deleted. The information for

unload carrier error was deleted.

e

Carrier identification error on page D-7

Unresponsive workstation When restarting an unresponsive workstation, do not select Disk Management from

the Windows Start menu.

e

To restart an unresponsive workstation (preferred method) on page D-15

Closing the Electronic

Signature Form

Do not click the × on the window to close the Electronic Signature Form.

e

To change a d onor status on page E-15

Reports The following information reports are now available:

o Invalid RMECs with Reason

o Invalid S-tubes with Reason

e

Report categories on page E-41

Default passwords The default AMPLILINK Software passwords for LABADMIN and LABUSER were

changed.

e

Operator access configuration on page E-92

Glossary The glossary was updated.

e

Glossary on page F-3

Deleted information The following information was deleted:

o Server backup kit

o DPX Library Plate workflow

Information corresponding to the deleted DPX Library Plate workflow was

removed from the following sections:

e

Secondary Pooling for reactive multi-sample pools on page A-34

e

Viability time on page A-96

e

Accepting results and transmitting them to the LIS on page A-182

e

Accepting results and transmitting them to the LIS on page A-206

e

Perform a Plate Run on page B-7

e

Perform a Batch Run on page B-11

e

Accepting and transmitting complete results on page B-71

o Formatting DVDs

o Tape backup kit for backing up PDM data

e

Backing up PDM data on page E-76

o To store backup media

o To clean the tape drive

cobas s 201 system Configuration E

Roche Diagnostics

16 Operator’s Manual · Version 2.0

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

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

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

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

5 Result assignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–77

6 PDM software introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–97

7 Pooling Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–109

8 Pooling Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–129

9 Data Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–175

10 AMPLILINK Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A–225

System Description

A

Roche Diagnostics

Operator’s Manual · Version 2.0 A-3

cobas s 201 system Configuration E 1 Safety

Table of contents

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 2.0

1 Safety cobas s 201 system Configuration E

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