Roche cobas 4800 Operator’s Manual

®
cobas
Operator’s Manual Software Version 2.1 for cobas® 4800 CT/NG Test
4800 System
cobas® 4800 System
CUS
®
CT/NG Test

Document information

Manual version Revision dates Main changes
1.1 May 2014 Change to error messages and reagent loading positions.
Table 1 Revision history
Edition notice Every effort has been made to ensure that the information contained in this manual is
accurate at the time of printing. Not all functionality described in this manual may be available to all users. Roche reserves the right to make any further required changes to software without prior notice. Such changes may not immediately be reflected in this document.
The screenshots in this publication have been added exclusively for the purpose of illustration. Configurable and variable data such as parameters, results, path names etc. visible therein must not be used for laboratory purposes.
Intended use
This manual is for users of the cobas® 4800 CT/NG Test on the cobas
Before using the test, it is important that the operator reads the cobas System Manual and this manual thoroughly.
U
For additional information, refer to the test-specific package insert.
Copyright © 2014 Roche Diagnostics International Ltd. All rights reserved.
Trademarks The following trademarks are acknowledged:
COBAS, COBAS X, COBAS Z, and LIFE NEEDS ANSWERS are trademarks of Roche.
All other trademarks are the property of their respective owners.
Feedback Every effort has been made to ensure that this manual fulfils the intended purpose as
mentioned above. All feedback on any aspect of this manual is welcome and will be considered during updates. Please contact your Roche representative, should you have any such feedback.
Instrument approvals This manual meets the European Standard EN ISO 18113-3.
Compliance is demonstrated by the following marks:
Complies with the IVD directive 98/79/EC.
®
4800 System.
®
4800 System
2 cobas® 4800 System, Operator’s Manual · Version 1.1
Issued by Underwriters Laboratories, Inc. (UL) for Canada and the US.
Abbreviations The following abbreviations are used:
Abbreviation Definition
PC
Table 2 Abbreviations
PreservCyt
®
cobas® 4800 System
CT/NG Test

Contact addresses

What is new in version 2.1

Workflow Recovery workflow run can be generated from a previously performed run within 24
hours. The PCR Only workflow has been renamed and improved to recovery workflow.
Roche Molecular Systems, Inc. 1080 US Highway 202 South Branchburg, NJ 08876 USA Made in Switzerland
Roche Diagnostics GmbH Sandhofer Strasse 116 68305 Mannheim Germany
U
For details, see About workflows (p. 10)
Result view notifications Icons help you identify if a result failed, is invalid, or has a flag. The result view also
highlights cells with positive results.
For details, see Results (p. 55)
U
Work orders The work order editor is now integrated into the software (sample editor). Barcodes
are automatically scanned during loading and used to generate a work order.
For details, see Sample editor (p. 51)
U
LIS You can see the LIS availability status and the transfer status. There is a status
displayed of results sent to the LIS.
For details, refer to the cobas® 4800 System System Manual.
U
Reports Reports have been improved. For example, better formatting, positive results are
highlighted.
Reagent use optimization Allows multiples (up to 3) of 24 reagent kits for master mix reagent and Mn reagent
to be loaded into the system.
U
For details, see To load the reagent carrier (p. 33)
Unloading samples You have the option to automatically unload the samples after they are pipetted and
before the run is over.
U
For details, see To load samples (p. 23)
Tracking of used tip racks. To reduce tip waste, partially used tip racks can be used in next run on the same
system. You can reuse partially used tip racks as long as enough tips are loaded. The software estimates how many tips are required for a run.
U
For details, see Loading the consumables (p. 27)
cobas® 4800 System, Operator’s Manual · Version 1.1 3
cobas® 4800 System
CT/NG Test
Usability Improved test selection dialog and filtering options.
For details, see To start a new run (p. 22)
U U For details, see Filtering and sorting runs and results (p. 58)
Test types CT/NG cytology and CT/NG non-cytology workflows can both be run by selecting
the CT/NG test.
4 cobas® 4800 System, Operator’s Manual · Version 1.1
cobas® 4800 System
Table of contents
CT/NG Test
Overview..................................................................................................................................7
General safety information.............................................................................................7
Overview of the test .........................................................................................................7
About specimen types .....................................................................................................7
About workflow types .....................................................................................................8
About the test concept.....................................................................................................8
About subtests............................................................................................................8
About reagents .................................................................................................................9
Workflow ..............................................................................................................................10
About workflows............................................................................................................10
Overview of full workflow ............................................................................................11
Full workflow short guide.......................................................................................12
Overview of recovery workflow...................................................................................14
Recovery workflow short guide .............................................................................15
Operation ..............................................................................................................................18
Safety information .........................................................................................................18
Performing a full workflow run...................................................................................18
Performing startup procedures..............................................................................18
Performing maintenance........................................................................................21
Removing the samples and reagents from storage..............................................21
Starting a new run....................................................................................................22
Loading samples.......................................................................................................23
Confirming or creating a work order file.............................................................25
Loading the consumables .......................................................................................27
Loading the reagents ...............................................................................................28
Starting the sample preparation run .....................................................................34
Unloading the microwell plate...............................................................................36
Sealing the microwell plate.....................................................................................37
Removing used reagents, samples, and deepwell plate.......................................38
Starting amplification and detection run .............................................................38
Reviewing and accepting results............................................................................39
Sending results to LIS..............................................................................................40
Unloading the analyzer...........................................................................................41
Performing shutdown procedure ..........................................................................41
Performing a recovery workflow run..........................................................................42
Starting a recovery workflow run ..........................................................................43
Selecting the run to recover and adding new IDs ...............................................43
Printing the microwell plate layout.......................................................................44
Removing the deepwell plate .................................................................................45
Setting up microwell plate......................................................................................45
Performing manual PCR setup..............................................................................45
Sealing the microwell plate.....................................................................................46
Centrifuging the microwell plate...........................................................................47
cobas® 4800 System, Operator’s Manual · Version 1.1 5
cobas® 4800 System
CT/NG Test
Starting amplification and detection run .............................................................47
Reviewing and accepting results............................................................................48
Sending results to LIS..............................................................................................49
Unloading the analyzer...........................................................................................50
Performing shutdown procedure ..........................................................................50
Sample editor..................................................................................................................51
About messages in the sample editor....................................................................51
Using the sample editor to create a work order file............................................52
Editing an existing work order file........................................................................54
Loading a work order file .......................................................................................55
Results..............................................................................................................................55
Reviewing results .....................................................................................................56
Grouping results ......................................................................................................57
Searching results ......................................................................................................57
Filtering and sorting runs and results...................................................................58
Accepting results......................................................................................................58
Printing results.........................................................................................................58
Creating result filters...............................................................................................60
Aborting a run................................................................................................................62
Configuration .......................................................................................................................63
Changing your password ..............................................................................................63
Troubleshooting...................................................................................................................64
List of error messages ....................................................................................................64
List of result flags ...........................................................................................................67
Revisions................................................................................................................................70
6 cobas® 4800 System, Operator’s Manual · Version 1.1
cobas® 4800 System Overview
CT/NG Test General safety information

Overview

General safety information

Test-specific safety information is contained in this manual. For general safety
®
4800

Overview of the test

information (e.g. safety classifications, safety precautions), read the cobas System System Manual.
The cobas® 4800 CT/NG Test is an in vitro nucleic acid amplification test for the qualitative detection of Chlamydia trachomatis (CT) and/or Neisseria gonorrhoeae (NG) in patient specimens.
The following sample carrier can be used for CT/NG testing: o PreservCyt® carrier with PreservCyt
®
primary containers
o 24-position sample carrier with primary cobas® PCR Media tubes or secondary
tubes
U
For more information about the test (e.g. minimum sample volumes), refer to the test­specific package insert.

About specimen types

WARNING
The following specimen types are supported:
Test type Specimen type Abbreviation Carrier used
CT/NG Swab - 24-position sample carrier
Urine - 24-position sample carrier
PreservCyt® PC
o PreservCyt® carrier
(primary tubes)
o 24-position sample
carrier (secondary tubes)
Table 3 Specimen types
Incorrect results due to use of non-approved specimen types
Supported specimen types may vary by region. Refer to the test-specific package insert for your region for supported specimen types.
r Use only specimen types that are approved by Roche.
U For details about the types of secondary tubes you can use, refer to the test-specific
package insert.
cobas® 4800 System, Operator’s Manual · Version 1.1 7
Overview cobas® 4800 System
About workflow types CT/NG Test

About workflow types

Two workflow types are supported. The workflow type has to be selected at the start of a new run.
Full workflow The full workflow covers sample preparation on the cobas x 480 instrument and
amplification and detection on the cobas z 480 analyzer.
Recovery workflow The recovery workflow allows you to recover aborted runs which were pipetted
correctly into the deepwell plate or microwell plate. For example, you drop the microwell plate while transferring it to the analyzer.
You manually pipette residual eluate from the deepwell plate into the new microwell plate and add new master mix reagent and Mn reagent.
To recover a run, the following criteria must be fulfilled:
o Instrument and analyzer are turned on and maintenance has been performed. o A full workflow run has been performed and the samples successfully prepared. o A full workflow run has been performed in the last 24 hours. o A full workflow run has been aborted by a user (M2 flag) or the analyzer (Z1 flag).

About the test concept

The recovery workflow run is only validated to work with extract from an instrument.
U
For stability of eluates, refer to the test-specific package insert.
Figure 1 Workflow and test type selection at the start of a new run
Tests are run in batches.
For more details about batch sizes, throughput, or mixed batch runs, refer to the test-
U
specific package insert.
About subtests
The analyzer can simultaneously detect signal from one or more detection channels, which makes it possible to obtain more information from a single reaction. This provides multiple subtests for each test type.
Subtests can be ordered for each sample individually using the sample editor.
U
For information about the sample editor, see Sample editor (p. 51)
8 cobas® 4800 System, Operator’s Manual · Version 1.1
cobas® 4800 System Overview
CT/NG Test About reagents
The following subtests are available:
Main test type Subtests Results
CT/NG CT and NG in combination CT/NG
CT only CT
NG only NG
Table 4 Subtests

About reagents

Reagent kit sizes Individual reagent kits are available for the following run sizes:
o 10 runs with 24 samples (up to 22 patient specimens plus 2 controls) o 10 runs with 96 samples (up to 94 patient specimens plus 2 controls)
NOTICE
Kit size
o Make sure that the kit size corresponds to the intended run size. Although not an
optimal use of reagents, a 96 kit size can be used for a 24 run.
o For the most efficient reagent utilization, it is advisable to maximize the number of
patient specimens processed within a run. Remaining reagents cannot be used later for another run.
Reagent handling Some reagents are poured into reagent reservoirs and then placed onto their
dedicated positions on the reagent reservoir carriers.
Other reagents are ready to use. They are decapped and then placed onto their dedicated positions on the reagent carrier.
Reagent expiry time zone offset
The reagent expiry date is based on the Coordinated Universal Time (UTC). The local time
CAUTION
for reagent expiry could be offset by plus or minus 12 hours, depending on the local time zone relative to UTC.
r Check the reagent expiry date and consider that it is based on UTC.
U For instructions on handling and storage of reagents, refer to the test-specific package
insert.
Controls Two external controls (positive control and negative control) are provided in a
control kit. Controls are always processed on position A1 and B1 respectively of the deepwell and microwell plates.
All controls are homogeneous and do not require vortexing or shaking prior to loading on the instrument.
U
For instructions on handling and storage of controls, refer to the test-specific package insert.
Controls are loaded on the reagent carrier not the sample carrier.
Q
cobas® 4800 System, Operator’s Manual · Version 1.1 9
Workflow cobas® 4800 System
About workflows CT/NG Test

Workflow

In this chapter the different workflows are described.

About workflows

The following workflow types are available.
Workflow Description Ordering
Full workflow (with or without LIS)
Recovery workflow (with or without LIS)
Table 5 Workflow types
Sample preparation and amplification and detection
Manual PCR setup and amplification and detection
LIS or work order file
-
10 cobas® 4800 System, Operator’s Manual · Version 1.1
cobas® 4800 System Workflow
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CT/NG Test Overview of full workflow

Overview of full workflow

The full workflow with and without LIS is shown below.
Figure 2 Full workflow (with and without LIS)
cobas® 4800 System, Operator’s Manual · Version 1.1 11
Workflow cobas® 4800 System
Overview of full workflow CT/NG Test
Infection by samples and associated materials due to inappropriate laboratory practices
WARNING
Follow Good Laboratory Practices, especially when working with biohazardous material. If Good Laboratory Practices are not followed, contact with biohazardous material may occur, resulting in infection.
r Do not eat, drink, or smoke in laboratory work areas. r Wear lab gloves and lab coats whenever preparing consumables, reagents, samples, or
when cleaning.
r Wear eye protection when handling samples. Wash hands thoroughly afterwards.
Full workflow short guide
The following short guide is a summary of the workflow without details.
For a complete and detailed description of the workflow, see Performing a full workflow
U
run (p. 18)
Step User action
1
Start up the system. Switch on the analyzer, heater/shaker unit, and
instrument
1. Switch on the analyzer.
2. Switch on heater/shaker unit.
3. Switch on the instrument.
Start up and log on to the software
1. Switch on the monitor and control unit.
2. Log on to the software.
2
Perform instrument maintenance.
1. Choose Overview > System > cobas x 480 tab and check maintenance status of the instrument.
o If weekly maintenance is due, choose the
Perform weekly maintenance button.
o If daily maintenance is due, choose the Perform
daily maintenance button.
Follow the instructions displayed on the monitor.
3
Remove samples and reagents from storage.
4
Start new run. 1. Choose (New run).
Table 6 Full workflow short guide (with or without LIS)
12 cobas® 4800 System, Operator’s Manual · Version 1.1
U For instructions on storage and handling of
reagents, samples and controls, refer to test­specific package insert.
2. Select the Full option.
3. Select the CT/NG check box.
4. Optionally, type a run name.
5. Choose the OK button.
cobas® 4800 System Workflow
CT/NG Test Overview of full workflow
Step User action
5
Load samples. 1. Decap samples.
2. Place samples on corresponding carrier.
3. Insert sample carriers on autoload tray.
4. Choose the Load specimen button.
6
With LIS, confirm the work order or Without LIS, create the work order.
7
Load consumables. 1. Place listed consumables on appropriate
With LIS:
1. Confirm the work order and choose the Next button.
or
Without LIS:
1. Define the type of specimen.
2. Define the requested result.
3. Choose the Next button.
carriers.
2. Insert carriers on autoload tray.
3. Choose the Load consumables button.
8
Load reagents. 200 mL reagent reservoir carrier
1. Load wash buffer reagent 200 mL on reagent reservoir carrier as indicated in the wizard (scan-scan-pour-place principle).
2. Insert carrier on autoload tray.
3. Choose the Load reagents button.
50 mL reagent reservoir carrier
1. Load reagents on 50 mL reagent reservoir carrier as indicated in the wizard (scan-scan­pour-place principle).
2. Insert carrier on autoload tray.
3. Choose the Load reagents button.
Reagent carrier
1. Open reagent vials and load them on reagent carrier as indicated in the wizard.
2. Insert carrier on autoload tray.
3. Choose the Load reagents button.
9
Start sample preparation run. 1. Choose the Start run button.
The sample preparation starts.
2. Check the timer in the wizard.
Table 6 Full workflow short guide (with or without LIS)
cobas® 4800 System, Operator’s Manual · Version 1.1 13
Workflow cobas® 4800 System
Overview of recovery workflow CT/NG Test
Step User action
10
Unload and seal microwell plate. 1. To review the results of the sample preparation,
choose the Sample Preparation results button.
2. Choose the Unload button.
3. Seal the microwell plate as indicated on screen.
4. Choose the Next button.
11
Remove used reagents, samples, and deepwell plate.
12
Load microwell plate on to the analyzer.
1. Remove used reagents, samples, and deepwell plate from the instrument.
1. Press the load button on the analyzer.
2. Place the sealed microwell plate into the microwell plate loader.
3. Press the load button again. The amplification and detection run starts automatically.
4. Check the timer in the wizard.
13
Review result and accept results. 1. Choose the Show result button.
2. Review and accept results in Results work area.
3. Select results and choose (Print) to print the results report, if required.
14
With LIS, send the results to LIS. Consider that depending on the configuration, all
results are transferred to LIS or only accepted results are transferred to LIS. Control results are always uploaded to LIS.
1. Select a result or group of results and choose the Send results to LIS button.
15
Unload the microwell plate from the analyzer.
Table 6 Full workflow short guide (with or without LIS)
1. Unload the microwell plate from the analyzer as soon as is practical after the run has finished.
2. Discard the microwell plate according to the appropriate local regulations.

Overview of recovery workflow

The recovery workflow allows you to recover failed runs where the sample has been successfully prepared. A run can only be recovered one time.
The recovery workflow is shown below.
14 cobas® 4800 System, Operator’s Manual · Version 1.1
cobas® 4800 System Workflow
Sample preparation cobas
x 480 instrument
Sample and reagent handling
area
cobas 4800 software
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cobas z 480 analyzer
1
Start recovery run
5
Remove deepewell plate
6
Load microwell plate into analyzer
2
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3
Print plate layout report
4
Get deepwell plate
5
Set up microwell plate
7
Review results
9
Unload analyzer
8
With LIS: send results to LIS
CT/NG Test Overview of recovery workflow
Figure 3 Recovery workflow
Recovery workflow short guide
CAUTION
Infection by samples and associated materials due to inappropriate laboratory practices
Follow Good Laboratory Practices, especially when working with biohazardous material. If Good Laboratory Practices are not followed, contact with biohazardous material may occur, resulting in infection.
r Do not eat, drink, or smoke in laboratory work areas. r Wear lab gloves and lab coats whenever preparing consumables, reagents, samples, or
when cleaning.
r Wear eye protection when handling samples. Wash hands thoroughly afterwards.
The following short guide is a summary of the workflow without details.
For a complete and detailed description of the workflow, see Performing a recovery
U
workflow run (p. 42)
cobas® 4800 System, Operator’s Manual · Version 1.1 15
Workflow cobas® 4800 System
Overview of recovery workflow CT/NG Test
Step User action
1
Start a recovery workflow run. 1. Choose (New run).
2. Select the Recovery option.
3. Select the CT/NG check box.
4. Optionally, type a run name.
5. Choose the OK button.
2
Select the run to recover and add new IDs
3
Print the microwell plate layout. 1. To print the work order file for microwell plate
1. Choose the run to recover.
2. In the Microwell plate ID field, scan the microwell plate barcode.
3. In the Master Mix ID field, scan the master mix reagent barcode.
4. In the Mn Reagent ID field, scan the Mn reagent barcode.
setup, choose (Print) from the global navigation bar.
2. In the software, choose the Next button.
4
Get the deepwell plate.
1. Do one of the following:
o If the deepwell plate has been unloaded by
the instrument, remove it from the plate carrier, or
o If the deepwell plate has been stored, get it
from storage, or
o If the deepwell plate has not been unloaded
by the instrument, unload the deepwell plate manually.
U For details how to unload the instrument
manually, refer to the cobas System Manual.
5
Set up the new microwell plate. 1. Pipette the reagents and prepared specimens
into the microwell plate in accordance with the microwell plate layout and the description in the test-specific package insert.
2. Seal the microwell plate.
3. If necessary, log back on to the software.
4. In the software, choose the Next button.
6
Load microwell plate into the analyzer.
1. Press the load button on the analyzer.
2. Place the sealed microwell plate into the microwell plate loader.
3. Press the load button again. The amplification and detection run starts automatically.
4. Check the timer in the wizard.
®
4800 System
Table 7 Recovery workflow short guide
16 cobas® 4800 System, Operator’s Manual · Version 1.1
cobas® 4800 System Workflow
CT/NG Test
Step User action
7
Review and accept results. 1. Choose the Show result button.
2. Review and accept results in Results work area.
3. Select results and choose (Print) to print the results report, if required.
8
With LIS, send the results to LIS. Consider that depending on the configuration, all
results are transferred to LIS or only accepted results are transferred to LIS. Control results are always uploaded to LIS.
1. Select a result or group of results and choose the Send results to LIS button.
9
Unload the microwell plate from the analyzer.
Table 7 Recovery workflow short guide
1. Unload the microwell plate from the analyzer as soon as is practical after the run has finished.
2. Discard the microwell plate according to the appropriate local regulations.
cobas® 4800 System, Operator’s Manual · Version 1.1 17
Operation cobas® 4800 System
Safety information CT/NG Test

Operation

In this chapter the operation of the system is described.

Safety information

Considerations before operation
Make sure that you have read and understood the chapter General safety information in the cobas®4800 System System Manual. The following safety messages in particular are relevant:
r Warning messages:
o Loss of sight due to staring into the laser beam o Infection by samples and associated materials o Infection and injury due to sharp objects o Infection by biohazardous waste o Contamination of the environment by liquid waste and solid waste
r Caution messages:
o Personal injury due to contact with moving parts o Skin inflammation or injury caused by reagents o Personal injury due to hot surface
r Safety precautions:
o Operator qualification
r Observe the illustrated system safety labels from the cobas
Manual
®
4800 System System

Performing a full workflow run

The following procedures guide you through all required steps to perform a full workflow run with sample preparation on the instrument and amplification and detection on the analyzer. The procedures cover both working modes: with and without LIS. Steps that only apply to one working mode are indicated accordingly.
Performing startup procedures
NOTICE
18 cobas® 4800 System, Operator’s Manual · Version 1.1
Instrument damage due to improper handling
To prevent hardware damage, follow the steps in the exact order outlined when starting up the system.
To start up the system, it is important that you perform the following steps in this exact order:
1. Switch on the analyzer.
2. Switch on the heater/shaker unit.
3. Switch on the instrument.
4. Start up the software.
cobas® 4800 System Operation
A
A
CT/NG Test Performing a full workflow run
P To switch on the analyzer
1
Switch on the analyzer. The power switch is located at the back of the analyzer.
The analyzer is powered on and initializes.
A Power switch of the analyzer
Figure 4 Switching on the analyzer
S
P To switch on the heater/shaker unit
1
Switch on the heater/shaker unit. The switch is located at the front of the heater/shaker controller box.
A Power switch of heater/shaker controller box
Figure 5 Switching on the heater/shaker unit
S
cobas® 4800 System, Operator’s Manual · Version 1.1 19
Operation cobas® 4800 System
A
Performing a full workflow run CT/NG Test
P To switch on the instrument
1
Switch on the instrument. The power switch is located at the front of the instrument.
The instrument is powered on and initializes.
WARNING
A Power switch of the instrument
Figure 6 Switching on the instrument
Delay of results due to improper handling
Turning the power of the instrument off during a run can lead to a sample rerun.
r Do not turn off the instrument power during a run.
S
P To start up and log on to the software
1
Switch on the monitor and control unit.
After the Windows operating system starts, double-click the cobas 4800 v2.1 desktop icon to open the software.
The software displays the System overview tab.
2
Choose (Log on) to log on and enter your assigned user ID and password.
3
Choose the OK button.
Q
o The user ID is not case-sensitive. o The password is case-sensitive. The password displays as asterisks when typed to
maintain security.
S
20 cobas® 4800 System, Operator’s Manual · Version 1.1
cobas® 4800 System Operation
CT/NG Test Performing a full workflow run
Performing maintenance
Periodic maintenance needs to be performed in order to ensure safe and reliable operation of the instrument.
NOTICE
Periodic maintenance
o Performing daily and weekly maintenance is mandatory. A sample preparation run can
only be started when maintenance is done.
o If any parts of the instrument or carriers have become contaminated, the weekly
maintenance procedure must be performed.
o Counters are reset to twenty-four hours when daily maintenance is performed. If
weekly maintenance is being performed, daily maintenance is not required on that day.
P To perform daily or weekly maintenance on the instrument
1
To check the maintenance status, choose Overview > System > cobas x 480 tab.
Figure 7 Checking the maintenance status
2
Do one of the following: o If the weekly maintenance is due, choose the Perform weekly maintenance
button and follow the instructions displayed on the monitor.
U
For more details about weekly maintenance, refer to the cobas®4800 System System Manual.
o If the daily maintenance is due, choose the Perform daily maintenance
button and follow the instructions displayed on the monitor.
For more details about daily maintenance, refer to the cobas®4800 System System
U
Manual.
S
Removing the samples and reagents from storage
The reagents that you need to perform the run depends on the run size.
U
For instructions on storage and handling of reagents, samples and controls, refer to test­specific package insert.
cobas® 4800 System, Operator’s Manual · Version 1.1 21
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