Roche cobas s 201 system User manual

Brand: Roche

Model: cobas s 201 system

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.

cobas s 201 System 0

Operator’s Manual for Use with Large Pools

(Pools of 24, 48, and 96)

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:

Pooling and Data Management

(PDM)

Roche Molecular Systems, Inc.

Branchburg, NJ

USA

Hamilton Microlab STAR IVD /

STARlet IVD Pipettor

Hamilton Company

Bonaduz

Switzerland

COBAS® AmpliPrep Instrument Roche Diagnostics Ltd.

CH-6343 Rotkreuz

Switzerland

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.

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

Roche cobas s 201 system User manual

Roche cobas s 201 system User manual

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