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Roche cobas s 201 system User manual

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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.
Copyright © 2014-2019, F. Hoffmann-La Roche Ltd. All rights reserved.
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
Table of contents
/