Roche cobas s 201 system User manual

Type
User manual

Roche cobas s 201 system is a versatile tool for automating nucleic acid testing. It offers various pooling algorithms, including primary pooling, 2D pooling, confirmation pooling, and resolution pooling, to optimize testing efficiency and reduce costs. The system's batch concept allows for flexible sample processing, and it can accommodate different plate sizes (24, 48, and 96 wells). Whether you're looking for high-throughput screening or confirmatory testing, the cobas s 201 system provides a comprehensive solution for your molecular testing needs.

Roche cobas s 201 system is a versatile tool for automating nucleic acid testing. It offers various pooling algorithms, including primary pooling, 2D pooling, confirmation pooling, and resolution pooling, to optimize testing efficiency and reduce costs. The system's batch concept allows for flexible sample processing, and it can accommodate different plate sizes (24, 48, and 96 wells). Whether you're looking for high-throughput screening or confirmatory testing, the cobas s 201 system provides a comprehensive solution for your molecular testing needs.

3
0
0
cobas s 201 System 0
Operator’s Manual for Use with Large Pools
(Pools of 24, 48, and 96)
0
P/N: 05216451190-01
0.2 07/2008, version 1.0
This manual is for use with Configuration C of the cobas s 201 system.
Preface
07/2008, version 1.0 0.3
Table of Contents
Preface
Table of Contents ..........................................................................0.3
Revision History ............................................................................ 0.4
How to Use this Manual ............................................................... 0.6
Conventions Used in This Manual ............................................... 0.7
Glossary ........................................................................................ 0.12
Precautions ..................................................................................0.19
1. Pooling Algorithms
Overview ........................................................................................ 1.1
Plate Run ........................................................................................ 1.3
Batch Run ...................................................................................... 1.4
2D Pooling ..................................................................................... 1.5
Confirmation Pooling .................................................................1.13
Resolution Pooling ...................................................................... 1.14
2. Pipetting
Batch Concept ...............................................................................2.1
Roche-Manufactured External Controls (RMECs) ..................... 2.2
User-Defined External Controls (UDECs) ..................................2.2
Deep-Well Plates ...........................................................................2.3
Primary Pools ................................................................................2.4
Repeat Batch Run ..........................................................................2.7
2D Pooling ..................................................................................... 2.8
Confirmation Pooling .................................................................2.11
Resolution Pooling ...................................................................... 2.14
Handling of Pipetting Errors.......................................................2.15
3. Workflow
Perform Primary Pooling .............................................................. 3.2
Perform Sample Preparation, Amplification, Detection ........... 3.18
Review and Release Donor Samples ...........................................3.32
Perform Secondary Pooling ........................................................3.35
Perform End of Day Processing .................................................. 3.38
4. Index
0.4 07/2008, version 1.0
Revision History
Manual Revision Revision Date
1.0 July 2008
Roche Molecular Systems, Inc.
Branchburg, NJ
USA
Distributed by
Roche Diagnostics
Indianapolis, IN 46256 USA
(For Technical Assistance call the
Roche Response Center
toll-free 1-800 526 1247)
Roche Diagnostics
H7V 4A2 Laval, Quebec
(For Technical Assistance call:
Pour toute assistance technique,
appeler le: 1-877 273 3433)
Roche Diagnostics (Schweiz) AG
CH-6343 Rotkreuz
Roche Diagnostics
F-38240 Meylan
Roche Diagnostics GmbH
D-68298 Mannheim, Germany
Distributore in Italia:
Roche Diagnostics SpA
Piazza Durante 11
I-20131 Milano
Roche Diagnostics S.L.
E-08006 Barcelona
Distribuidor em Portugal:
Roche Farmacêutica Química, Lda
P-2700 Amadora
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:
l
Pooling and Data Management
(PDM)
Roche Molecular Systems, Inc.
Branchburg, NJ
USA
l
Hamilton Microlab STAR IVD /
STARlet IVD Pipettor
Hamilton Company
Bonaduz
Switzerland
l
COBAS® AmpliPrep Instrument Roche Diagnostics Ltd.
CH-6343 Rotkreuz
Switzerland
l
COBAS® TaqMan® Analyzer Roche Diagnostics Ltd.
CH-6343 Rotkreuz
Switzerland
Preface
07/2008, version 1.0 0.5
Questions or comments regarding the contents of this manual can be
directed to the address below or to your Roche representative.
Roche Molecular Systems, Inc.
4300 Hacienda Drive
Pleasanton, California 94588-2722
ROCHE, AMPERASE, AMPLILINK, COBAS, COBAS S, AMPLIPREP and
TAQMAN are trademarks of Roche.
ROCHE RESPONSE CENTER is a servicemark of Roche.
Microlab is a registered trademark of Hamilton Company.
Microsoft, Windows, and Windows XP are either registered trademarks or
trademarks of Microsoft Corporation in the United States and/or other
countries.
Oracle is a registered trademark of Oracle Corporation.
AMPLILINK Software:
The Source Code version of the executable code (the "Software") is
available under the terms of the Interbase Public License Version 1.0. The
user may obtain a copy of the license at:
http://interbase.com/IPL.html.
The Software is offered solely under the terms of the Interbase Public
License Version 1.0.
Copyright © 2008, Roche Molecular Systems, Inc. All rights reserved.
0.6 07/2008, version 1.0
How to Use this Manual
Before operating the cobas s 201 system, it is essential that the warnings,
cautions, and safety requirements contained in this manual are read and
understood by the user.
Refer to the section titled Symbols on page 0.8 for a description of the
warning symbols and caution symbols that appear in this manual.
Preface (Preface) summarizes safety precautions necessary when
installing, operating, and servicing the system.
Section 1 (Pooling Algorithms) describes the Primary Pooling and
Secondary Pooling methods and testing algorithms.
Section 2 (Pipetting) explains the batch concept and pipetting
operations.
Section 3 (Workflow) describes routine workflow procedures.
Index
Preface
07/2008, version 1.0 0.7
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:
Text convention Used for
Numbered lists Numbered procedures that should be
implemented in order during an operation:
1. Display the Donor Review tab.
2. Select the desired status filter.
Bold typeface Emphasis of any term or component that is
being described:
The Library Plate is used to store samples for
later testing.
Italics Designating another section of this manual
that should be consulted, or designating the
name of a screen.
Refer to the section titled Symbols on page
0.8 for a description of the warning symbols.
> Separates command options in a multi-level
command:
Select File > Shut Down from the menu bar.
0.8 07/2008, version 1.0
Symbols
Certain symbols are used throughout this manual to provide a ready
visual reference. These symbols are as follows:
Symbol Used for
Information note. Designates a note that
provides additional information concerning
the current topic or procedure.
Important note. Designates an important
note that must be reviewed and understood.
Warning. Indicates a possible hazardous
situation that, if not avoided, may result in
death or serious injury.
Caution. Indicates a possible hazardous
situation which, if not avoided, may result in
personal injury and/or in damage to the
system.
Warning Moving Parts. Indicates a possible
hazardous situation. Keep hands away from
moving parts.
Warning Hot Surface. Designates the
presence of a hot surface. Keep hands away
from hot surfaces.
Warning Laser Transmitter. Designates the
presence of a laser transmitter. Do not stare
into the laser transmitter.
Warning Potentially Biohazardous Material.
Indicates a possible hazardous situation due
to biohazardous material that may result in
death or serious injury.
Electrical and electronic equipment marked
with this symbol are covered by the European
directive WEEE. This symbol denotes that
the equipment must not be disposed of in the
municipal waste system.
(WEEE) Directive 2002/96/EC of the
European Parliament and the Council of 27
January 2003 on waste electrical and
electronic equipment
Preface
07/2008, version 1.0 0.9
The following symbols appear on the system type plate:
The following symbols appear on the Hamilton Microlab STAR IVD /
STARlet IVD Pipettor:
Caution: Refer to accompanying documents.
The triangular symbol on the back of an
instrument is a general reminder that users
read the safety information contained in this
manual. Users must be able to identify
specific hazards and take appropriate action
to avoid them.
Manufacturer of device.
Warning Laser Transmitter. Situated on the
barcode reader to designate the presence of a
laser transmitter. Do not stare into the laser
transmitter.
Caution. Situated on the paddles to indicate
a possible hazardous situation. Keep paddles
extended to avoid bumping into the loading
deck.
Caution. Situated on the right hand side of
the shield and on the pipettor arm to indicate
a possible hazardous situation. Keep hands
away from moving parts.
Warning Potentially Biohazardous Material.
Situated on the left hand side of the shield
and on the right hand side of the pipettor to
indicate that donor samples and the waste
bag may contain biohazardous material.
0.10 07/2008, version 1.0
The following symbols appear on the COBAS® AmpliPrep Instrument:
Warning Laser Transmitter. Situated on
Transfer Head 1 to designate the presence of
a laser transmitter. Do not stare into the laser
transmitter.
IEC 825-1: 1993
Class 1 Laser Product
Appareil à laser de classe 1
1550 nm < 10 mW
Caution. Situated behind the load panel to
indicate the type of laser used. Do not stare
into the laser transmitter.
Warning - Fire Hazard
For continued protection
replace only with same
type and rating of fuse.
War n in g. Situated below the power supply.
Only replace a fuse with a fuse of the same
type and rating.
Warning Potentially Biohazardous Material.
Situated behind the load panel, on the left
hand side of the instrument, to indicate that
K-tubes, S-tubes, and SPUs may contain
biohazardous material.
Preface
07/2008, version 1.0 0.11
The following symbols appear on the COBAS® TaqMan® Analyzer:
Warning Laser Transmitter. Situated on
the barcode scanner to designate the
presence of a laser transmitter. Do not
stare into the laser transmitter.
Warning Moving Parts. Situated on each
thermal cycler to indicate a possible
hazardous situation. Keep hands away
from moving parts.
Warning Hot Surface. Situated on each
thermal cycler to designate the presence of
a hot surface. Keep hands away from hot
surfaces.
War ning Biohaz ard . Situated behind the
load panel and on the service panel to
indicate that K-tubes may contain
biohazardous material.
0.12 07/2008, version 1.0
Glossary
The terminology that is used with the cobas s 201 system is generally the
same as that used in clinical laboratories. Certain specific terms, however,
are used for description of an operation or a component. A summary of
these terms and their definitions is provided below.
2D Pooling
Two-dimensional pooling. Secondary Pooling
on a reactive or invalid large Primary Pool
that creates
a matrix of donor pools where
each donor sample is pipetted into a unique
set of two separate pools such that if these two
pools are reactive, the results can be
attributed to a particular donor sample.
AmpErase AmpErase (Uracil-N-glycosylase) enzyme is
incorporated into Master Mix to selectively
destroy carryover products (containing
deoxyuridine) from previous amplification
reactions.
Amplification The process of producing many DNA copies
from a template DNA or RNA target region.
Amplification occurs on the COBAS®
TaqMan® Analyzer, where extracted samples
are heated and cooled in thermal cyclers
according to the Polymerase Chain Reaction
profile for the selected test.
Anneal The biochemical process of hybridizing or
binding two segments of complementary
nucleic acid by lowering temperature.
Confirmation Pooling Secondary Pooling on a reactive or invalid
large Primary Pool, where single-specimen
pools are created to confirm suspected
reactive donor samples and the remaining
samples are pipetted into multi-specimen
pools to confirm non-reactive test results.
Denaturation The biochemical process of separating double
stranded DNA into single strands, by
breaking the hydrogen bonds by raising
temperature.
Preface
07/2008, version 1.0 0.13
Detection Obtaining measurements to determine
whether a sample is reactive for the target
analyte. Fluorescence measurements are
made at selected temperatures and times
during the amplification process. When the
run is complete data are analyzed by the
AMPLILINK software to determine the
presence of the amplified products from the
target and internal control nucleic acid
sequences.
DNA Deoxyribonucleic Acid (DNA) is the genetic
material that is passed from parent to
daughter cells and propagates the
characteristics of the species in the form of
genes it contains and the proteins for which it
codes. DNA is built from the following four
kinds of nucleotides: dATP, dCTP, dTTP, and
dGTP.
Donor tube carrier Reusable carrier that is used to load and
unload donor tubes onto the Hamilton
Microlab STAR IVD / STARlet IVD Pipettor.
Donor tube A glass or plastic tube that contains a donor
specimen.
Extension Refers to the biological process of elongation
of the DNA chain that is being synthesized by
DNA polymerase using the parent DNA
strand as the template for the synthesis of the
daughter strand.
Extraction The process of isolating DNA or RNA for
subsequent molecular analysis. Pooled
samples undergo extraction on the COBAS®
AmpliPrep Instrument.
Intermediate Plate A 12 x 8 deep-well plate used to create interim
pools during the first phase of Primary
Pooling for large pools.
Internal control A built-in nucleic acid sequence that is
co-extracted and co-amplified with the
sample to monitor sample recovery and
amplification/detection inhibitions.
0.14 07/2008, version 1.0
K-carrier Reusable metallic holder that accommodates
up to 24 K-tubes that contain PCR-ready
samples for analysis on the COBAS®
TaqMan® Analyzer.
K-tip Kinetic Tip. Disposable tip that is used to
resuspend and transfer a prepared sample to a
K-tube.
K-tip rack A prepackaged disposable rack that holds 36
K-tips.
K-tube Kinetic tube. The disposable sample tube that
is used to amplify a prepared sample with
Master Mix. K-tubes come prepackaged in a
covered K-tube rack.
K-tube rack A prepackaged disposable rack that holds 96
K-tubes.
Library Plate A 12 x 8 deep well plate used to store aliquots
of donor samples in the event that testing
needs to be repeated.
LIS Laboratory Information System. A
computerized system for entering, managing,
and reporting laboratory information.
Information includes but is not limited to
donor demographics, test data, and
consumable inventory.
Magnetic glass particles Small magnetic particles, suspended in liquid,
that are used in combination with other
reagents to bind nucleic acids using positive
charge on the surface, allowing nucleic acids
to be separated from other sample
components by a magnet during washing.
MGP see Magnetic glass particles.
MPX A multiplexed set of targets that may include
HCV, HIV-1 Group M, HIV-1 Group O,
HIV-2, and HBV.
Preface
07/2008, version 1.0 0.15
PCR Polymerase Chain Reaction. The in vitro
biochemical process used to amplify short
specific target nucleic acid sequences. PCR is
performed by cycling the temperature of the
amplification mixture according to a set
profile. The profile generally consists of 1)
denaturation, 2) annealing, and 3) extension.
PDM Pooling and Data Management.
Plate carrier Reusable carrier that is used to load and
unload up to five plates onto the
Hamilton
Microlab
STAR IVD / STARlet IVD Pipettor.
Primary Pool A pool prepared by combining equal aliquots
from a specified number of donor tubes into
one S-tube. Once a sample has been
successfully aspirated by the system, that
sample is no longer eligible for Primary
Pooling.
Resolution Pool A single-specimen pool that is prepared from
either donor tubes or a Library Plate to retest
specimens with testing results that are either
reactive or invalid.
RF Radio frequency.
RMEC Roche-manufactured external control.
RMECs are mandatory for each batch.
Secondary Pooling Follow-up pooling performed to resolve
invalid or reactive initial test results.
S-tube Disposable sample tube. Empty, uncapped,
S-tubes are placed in barcode clips in an SK24
rack and loaded onto the Hamilton Microlab
STAR IVD / STARlet IVD Pipettor. After
pipetting is complete the S-tubes contain
pooled samples. The S-tubes are unloaded
from the Hamilton Microlab STAR IVD /
STARlet IVD Pipettor, capped, and loaded
onto the COBAS® AmpliPrep Instrument for
sample preparation. S-tubes are supplied in
bags of 24.
0.16 07/2008, version 1.0
S-tube carrier Reusable carrier that is used to load and
unload SK24 racks from the Hamilton
Microlab STAR IVD / STARlet IVD Pipettor.
Sample Refers generically to a donor specimen,
control reagents, or input sample (any pooled
or individual donor pipetted into an S-tube).
Sample processing unit Disposable device that contains the sample
and reagent mixture during sample
preparation. The SPU consists of two
processing chambers, the waste chamber, and
the sample tip chamber.
One SPU is used for each sample that is
processed.
Short Pool A short pool is a Primary Pool that contains
fewer than the planned 96, 48, or 24 samples.
A short pool is the result of a pipetting
error(s) during creation of a large Primary
Pool.
SK24 rack Reusable rack that holds S-tubes or K-tubes
in barcode clips. The SK24 rack loads and
unloads samples throughout the pipetting,
sample preparation, and amplification/
detection process.
Specimen Refers to a sample that has come from a
donor.
SPU see Sample processing unit.
SPU rack Reusable rack used to load 24 SPUs onto the
COBAS® AmpliPrep Instrument.
When sample preparation is complete, the
SPU rack contains the input S-tube and the
used SPUs. The SPUs contain the used K-tips
and all of the potentially biohazardous waste
in a chamber sealed by the used S-tip.
System Refers generically to the reagents, hardware,
and software for the cobas s 201 system.
Preface
07/2008, version 1.0 0.17
Test definition file File containing all the processing steps
required for sample preparation,
amplification, and detection. Test definition
files are provided by Roche on CD-ROM and
are loaded into AMPLILINK software.
Thermal cycler Programmable temperature block in the
COBAS® TaqMan® Analyzer. The thermal
cycler rapidly changes temperature according
to the amplification profile defined in the test
definition files.
Tip rack Disposable RNAse-free pipette tips are used
for sample and control pipetting on the
Hamilton Microlab STAR IVD / STARlet IVD
Pipettor. Pipette tips are packaged in
disposable tip racks. Each rack holds 96
pipette tips.
Tip carrier A carrier that is used to load and unload up to
five tip racks onto the Hamilton Microlab
STAR IVD / STARlet IVD Pipettor.
UDEC User-defined external control that can be
included in a batch. UDEC test results are not
included in the batch analysis.
UPS Uninterruptible power supply.
Viability time The elapsed time between initial pipetting
and assignment of final results.
If a result is not accepted within the viability
time limit, the sample is automatically
assigned a status of Complete, Unresolved,
unless the sample tested reactive in an
individual pool (Primary Pool of 1 or
Resolution Pool). In that case, the sample is
automatically assigned a status of Complete,
Reactive.
WNV West Nile virus. The West Nile virus belongs
to the Japanese Encephalitis Virus group of
the family Flaviviridae.
0.18 07/2008, version 1.0
Units
The following measurement abbreviations are used:
kg Kilogram
mL Milliliters (10
-3
liters)
VVolts
Preface
07/2008, version 1.0 0.19
Precautions
Safety Requirements
The safety precautions that are necessary when installing, operating,
and servicing the instruments are summarized in the following section
of this manual. It is important that you carefully read and understand
the statements regarding safety contained in these sections. This
information should also be made available to new employees and for
future reference.
For reasons of data security and integrity, it is required to use the
system with an uninterrupted power supply (UPS) as a loss of power
may cause data corruption or loss.
General Instrument Warnings
User should keep hands away from hot surfaces.
User should not stare into the laser transmitter when the barcode
readers are exposed.
User should keep hands away from moving parts.
Never remove the middle grounding prong from the power cable or
defeat its purpose by using an ungrounded adapter.
Disposal Recommendations
All electrical and electronic products should be disposed of separately
from the municipal waste system. Proper disposal of your old appliance
prevents potential negative consequences for the environment and
human health.
0.20 07/2008, version 1.0
Disposal of the Instrument
The instrument must be treated as biologically contaminated-
hazardous waste. Decontamination (i.e., a combination of processes,
including cleaning, disinfection and/or sterilization) is required before
reuse, recycling or disposal.
Dispose the instrument according to local and/or labor regulations. For
more information, contact your local Roche Support personnel.
Disposal of Control Unit Components
Components of your control unit such as the computer, monitor,
keyboard, etc. which are marked with the crossed-out wheeled bin
symbol are covered by the European Directive 2002/96/EC (WEEE).
These items must be disposed of via designated collection facilities
appointed by government or local authorities.
For more information about disposal of your old product, please
contact your city office, waste disposal service or your local Roche
Support personnel.
Constraint
It is left to the responsible laboratory organization to determine
whether control unit components are contaminated or not. If
contaminated, treat in the same way as the instrument.
Hamilton Microlab STAR IVD / STARlet IVD Pipettor
The Hamilton Microlab STAR IVD / STARlet IVD Pipettor conforms to
European norms as regards interference immunity. However, if the
Hamilton Microlab STAR IVD / STARlet IVD Pipettor is subjected to
electromagnetic RF fields, or if static electricity is discharged directly
onto the Hamilton Microlab STAR IVD / STARlet IVD Pipettor, its
liquid level detection ability may be negatively affected. It is therefore
recommended that the Hamilton Microlab STAR IVD / STARlet IVD
Pipettor be kept away from other equipment that emits electromagnetic
RF fields in the laboratory, and that static electricity be minimized in its
immediate environment.
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Roche cobas s 201 system User manual

Type
User manual

Roche cobas s 201 system is a versatile tool for automating nucleic acid testing. It offers various pooling algorithms, including primary pooling, 2D pooling, confirmation pooling, and resolution pooling, to optimize testing efficiency and reduce costs. The system's batch concept allows for flexible sample processing, and it can accommodate different plate sizes (24, 48, and 96 wells). Whether you're looking for high-throughput screening or confirmatory testing, the cobas s 201 system provides a comprehensive solution for your molecular testing needs.

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