cobas
®
4800 System
Operator’s Manual
Software Version 2.1 for
cobas® PIK3CA Mutation Test
For Research Use Only
Not for use in diagnostic procedures
cobas® 4800 System
PIK3CA Mutation Test RUO
Roche Diagnostics
2 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Document information
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® PIK3CA Mutation Test on the cobas
®
4800
System.
For Research Use Only. Not for use in diagnostic procedures.
Before using the test, it is important that the operator reads the cobas z 480 analyzer
Instrument Manual and this manual thoroughly.
Copyright © 2014 Roche Diagnostics International Ltd. All rights reserved.
Trademarks The following trademarks are acknowledged:
COBAS, 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:
Manual version Software version Revision dates Main changes
1.0 2.1 February 2014 Software update from 2.0 to 2.1
Table 1 Revision history
Issued by Underwriters Laboratories, Inc. (UL) for Canada and the US.
CUS
®
Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 3
cobas® 4800 System
PIK3CA Mutation Test RUO
Product names Except where the context clearly indicates otherwise, this manual uses the following
descriptions:
Contact addresses
What is new in software version 2.1
Result view notifications Icons help you identify if a result failed, is invalid, or has a flag.
U
For details, see Result icons (p. 22).
LIS It is now possible to send results to the LIS. LIS availability and transfer status are
now displayed.
U
For details, see Sending results to LIS (p. 17) and refer to the cobas z 480 analyzer
Instrument Manual.
Reports Report formatting has been improved.
Usability Improved test selection dialog and filtering options.
U
For details, see To start a new run (p. 12)
U For details, see Filtering and sorting runs and results (p. 24)
Product name Abbreviation
cobas
®
4800 software
software
cobas
®
4800 System
system
cobas z 480 analyzer analyzer
Table 2 Product names
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
cobas® 4800 System
PIK3CA Mutation Test RUO
Roche Diagnostics
4 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Table of contents
General safety information ...................................................................................................5
Workflow ................................................................................................................................6
PCR Only run...................................................................................................................6
PCR Only run short guide........................................................................................8
Operation ..............................................................................................................................10
Safety information .........................................................................................................10
Preparations for a run ...................................................................................................10
Performing startup procedures..............................................................................10
Performing a run............................................................................................................12
Set up the microwell plate ......................................................................................13
Sealing the microwell plate.....................................................................................15
Starting amplification and detection run .............................................................16
Reviewing and accepting results............................................................................17
Sending results to LIS..............................................................................................17
Unloading the analyzer...........................................................................................18
Performing shutdown procedure ..........................................................................19
Sample editor..................................................................................................................19
Using the sample editor to create a work order file............................................20
Editing an existing work order file........................................................................21
Loading a work order file .......................................................................................21
Results..............................................................................................................................22
Reviewing results .....................................................................................................23
Grouping results ......................................................................................................23
Searching results ......................................................................................................24
Filtering and sorting runs and results...................................................................24
Accepting results......................................................................................................24
Printing results.........................................................................................................25
Creating result filters...............................................................................................27
Configuration .......................................................................................................................30
Changing your password ..............................................................................................30
Troubleshooting...................................................................................................................31
Aborting a run................................................................................................................31
List of error messages ....................................................................................................31
List of result flags ...........................................................................................................34
Revisions................................................................................................................................36
Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 5
cobas® 4800 System General safety information
PIK3CA Mutation Test RUO
General safety information
Test-specific safety information is contained in this manual. For general safety
information (e.g. safety classifications, safety precautions), read the
cobas z 480 analyzer Instrument Manual.
Roche Diagnostics
6 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Workflow cobas® 4800 System
PCR Only run PIK3CA Mutation Test RUO
Workflow
The following workflow is available.
PCR Only run
The workflow for a PCR Only run is shown below.
For the PCR Only workflow, the test reagents and prepared specimens are manually
pipetted into the microwell plate (AD plate 0.3 mL).
U
For information on handling and preparing reagents and specimens, and how to pipette
them into the microwell plate, refer to the test-specific package insert.
Figure 1 Workflow for a PCR Only run
Workflow type Description Ordering
PCR Only run Amplification and detection
on the analyzer
Work order file or sample
editor. No LIS ordering.
Table 3 Workflow
1
Manually prepare
reagents and samples
2
Start new run
3
Create or load work order
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Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 7
cobas® 4800 System Workflow
PIK3CA Mutation Test RUO PCR Only run
WARNING
Infection by samples and associated materials due to inappropriate laboratory
practices
Follow standard laboratory practices, especially when working with biohazardous material.
If standard 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 protective disposable gloves and laboratory coats whenever preparing
consumables, reagents, samples, or when cleaning.
r Wear eye protection when handling samples. Wash hands thoroughly afterwards.
Roche Diagnostics
8 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Workflow cobas® 4800 System
PCR Only run PIK3CA Mutation Test RUO
PCR Only run short guide
The following short guide is a summary of the workflow without details.
U
For a complete and detailed description of the workflow, see Operation (p. 10).
Step User action
1
Manually prepare the reagents
and specimens.
1. Remove the reagents and specimens from
storage.
2. Manually prepare the reagents and specimens
according to the test-specific package insert.
2
Start a new run. 1. Choose the New run button.
2. Do one of the following:
o Select a test from the list.
o Select the Load work order file option,
load the required work order file, and
proceed to step 3, action 8 (paragraph
below).
3. Optionally, type a run name.
4. Choose the OK button.
3
Create the work orders. 1. Scan the microwell plate barcode into the
Microwell Plate ID field.
2. Scan the DNA sample preparation kit barcode
into the first DNA Sample Preparation Kit-ID
field.
3. Scan the barcode of the
cobas® PIK3CA Mutation Test kit into the first
PIK3CA Mutation Test Kit-ID field.
4. In the first Specimens field, enter the number
of specimens. Consider that you can enter up
to 24 specimens in each Specimens field. The
maximum number of specimens per run is 30.
You must enter a Sample ID for all specimens.
If you use more than one test kit, enter the kit
information sequentially (e.g. 1,2 not 1,3).
5. Scan the sample ID barcodes into the
Sample ID column in the lower part of the
screen.
6. If you use more than one test kit, repeat steps 2
to 5 for each test kit in the order described
above.
7. Choose the Save button. Save the file with the
default file name assigned by the software.
8. Choose (Print) to print the work order
file for microwell plate setup.
4
Set up the microwell plate. 1. Pipette the reagents and prepared specimens
into the microwell plate in accordance with the
printout of the work order file and the
description in the test-specific package insert.
2. Seal the microwell plate.
3. If necessary, log back into the software.
4. In the software, choose the Next button.
Table 4 PCR Only run short guide
Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 9
cobas® 4800 System Workflow
PIK3CA Mutation Test RUO
5
Load microwell plate on to 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 run starts automatically.
6
Review and accept results. 1. After the run has finished, 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.
7
With LIS, send the results to
LIS.
Consider that depending on the configuration, all
results are sent to LIS or only accepted results are
sent to LIS. Control results are always sent to LIS.
1. Select a result or group of results and choose
the Send results to LIS button.
8
Unload the microwell plate
from the analyzer.
1. Unload the microwell plate from the analyzer
as soon as is practical after the run has finished.
2. Check the microwell plate for indications of
leakage or evaporation.
3. Discard the microwell plate according to the
appropriate local regulations.
Step User action
Table 4 PCR Only run short guide
Roche Diagnostics
10 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Operation cobas® 4800 System
Safety information PIK3CA Mutation Test RUO
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 z 480 analyzer Instrument 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 z 480 analyzer Instrument
Manual.
Preparations for a run
Perform the following procedures before starting a run.
Performing startup procedures
To start up the system, you need to perform the following steps:
1. Switch on the analyzer.
2. Switch on the control unit.
3. Start up the software.
NOTICE
Instrument damage due to improper handling
To prevent hardware damage, follow the steps in the exact order outlined when starting up
the system.
Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 11
cobas® 4800 System Operation
PIK3CA Mutation Test RUO Preparations for a 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.
Figure 2 Switching on the analyzer
S
P To start up and log on to the software
1
Switch on the monitor and control unit.
2
To start the software, do one of the following:
o Double-click the cobas
®
4800 software icon on the desktop.
or,
o Open the Start menu and choose the cobas
®
4800 software icon.
3
Enter your assigned user ID and password.
4
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
P To manually prepare the reagents and specimens
1
Remove the reagents and specimens from storage.
U
For information on handling and preparing reagents and specimens, refer to the
test-specific package insert.
2
Manually prepare the reagents and specimens according to the instructions in the
test-specific package insert.
S
A Power switch of the analyzer
A
Roche Diagnostics
12 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Operation cobas® 4800 System
Performing a run PIK3CA Mutation Test RUO
Performing a run
A wizard guides you through the entire run, from preparation of the microwell plate
to amplification and detection on the analyzer.
U
For details, see PCR Only run short guide (p. 8)
Automatic log off The software will automatically log off the user after a certain period of inactivity if
the check box Enable automatic log off is selected in the user settings. Only users
with the Supervisor role can change these settings for their own user level and for the
Operator user level.
U
For information on how to change the settings of a user account, refer to the
Configuration chapter in the cobas z 480 analyzer Instrument Manual.
Using more than one kit If you use more than one DNA sample preparation kit, make sure to first enter the
specimens prepared with the first kit into the Sample ID column, then the specimens
prepared with the second kit and so on. For tracking purposes, specimens should be
separated according to the kits with which they were prepared.
Creating work order files with the
sample editor
You can use the sample editor to prepare one or more work order files before starting
a run, or to prepare a work order file for the next run while a run is still in progress. A
work order file can be selected in the Select test dialog box as described below.
U
For information about the sample editor, see Sample editor (p. 19).
NOTICE
Loss of reagents, samples, or consumables
Inappropriate user actions can cause loss off reagents, samples, or consumables.
r Do not disconnect the network cable during a run.
r It is not possible to go back to a previous step in a run. To avoid losing reagents,
samples, or consumables, follow the guidelines outlined in this manual.
P To start a new run
1
Choose (New run).
The Select test dialog box is displayed.
Figure 3 Select test dialog box
2
Select the PCR Only option.
Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 13
cobas® 4800 System Operation
PIK3CA Mutation Test RUO Performing a run
3
Select the PIK3CA RUO check box.
4
Optionally, enter a name for the run in the Run name field.
The system generates a generic run name if you leave the field empty. The generic
run name is composed of date and time when the test was selected and the test
name (e.g. "28-Mar-2013 13:39 PIK3CA").
5
Choose the OK button.
The Workplace tab is displayed showing the wizard for the new run.
S
Set up the microwell plate
NOTICE
Analyzer damage due to use of non-Roche consumables
Use of non-Roche consumables may damage the analyzer or lead to incorrect results.
r Use only Roche consumables designed for use on the system.
r When loading consumables, check that the consumables are not damaged. Do not use
damaged consumables. Do not reuse consumables from another system.
The microwell plate is barcoded and designed to be used only once. The software
tracks the use of the plate and rejects previously used microwell plates.
If an error happens while creating a work order file, the color of the field will change
to red. Move the mouse pointer over the red field to display a tool tip that gives
information about the nature of the error.
If the error happens in the sample ID area, an error message will be displayed above
the sample ID area, and no tool tip is displayed.
Figure 4 Creating a work order file for setting up the microwell plate
A Information about test type and run date E Fields for cobas® PIK3CA Mutation Test kit
B Fields for DNA sample preparation kit F Fields for number of specimens
C Field for barcode of microwell plate G Microwell plate layout
D Fields for specimens barcodes
A
E
B
C
D
G
F
Roche Diagnostics
14 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Operation cobas® 4800 System
Performing a run PIK3CA Mutation Test RUO
Q
o Make sure to enter the barcode of the cobas® PIK3CA Mutation Test kit into the field
next to the barcode of the DNA sample preparation kit which was used to prepare the
same set of specimens.
o Make sure to enter the kit barcodes into their relevant fields. Entering a barcode into a
wrong field will lead to an error.
o If no hand-held barcode reader is available, enter the barcodes manually and press the
Enter key after entering each barcode. When entering the barcodes, follow the order
described below.
P To create a work order file for microwell plate setup
1
Scan the microwell plate barcode into the Microwell Plate ID field.
2
Scan the barcode of the DNA sample preparation kit into the first field of the
DNA Sample Preparation Kit-ID column.
3
Scan the barcode of the cobas® PIK3CA Mutation Test kit into the first field of the
PIK3CA Mutation Test Kit-ID column.
4
In the first Specimens field, enter the number of specimens. Consider that you
can enter up to 24 specimens in each Specimens field. The maximum number of
specimens per run is 30. You must enter a Sample ID for all specimens. If you use
more than one test kit, enter the kit information sequentially (e.g. #1,#2 not
#1,#3).
5
Scan the sample ID barcodes into the Sample ID column in the lower part of the
screen.
U
For information about the pipetting order, refer to the test-specific package insert.
6
If you use more than one test kit, repeat steps 2 to 5 for each test kit in the order
described above.
7
After entering all sample IDs, choose the Save button to save the work order file,
if required.
Save the work order file with the default file name assigned by the software.
8
Choose (Print).
A printable work order file that shows the microwell plate layout is displayed. Use
this printout for pipetting the reagents and prepared samples into the microwell
plate.
9
Choose the Next button.
S
P To pipette the reagents and prepared specimens into the microwell plate
1
Pipette the reagents and specimens into the microwell plate in accordance with
the printout of the work order file and the description in the test-specific package
insert.
You can print the microwell plate layout which includes the test name and the
barcode of the ordered sample. Ensure that the eluate is transferred correctly to
the microwell plate and that the work order file correctly reflects the microwell
plate layout.
The work order file describes the layout of the microwell plate and shows which
specimens and reagents are to be pipetted into which well.
Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 15
cobas® 4800 System Operation
PIK3CA Mutation Test RUO Performing a run
U For information on handling and preparing reagents and specimens, and how to
pipette them into the microwell plate, refer to the test-specific package insert.
S
Sealing the microwell plate
After pipetting all reagents and prepared specimens into the microwell plate, the
microwell plate must be sealed properly with a sealing film. Sealing the microwell
plate is crucial to eliminate evaporation at high temperatures.
CAUTION
Incorrect results due to evaporation or contamination of specimens and controls
r Make sure that microwell plate and sealing film are not expired.
r Follow the outlined procedure to seal the microwell plate to prevent leakage of the
sealing film, evaporation or contamination of specimens and controls. Plate leakage
can contaminate the analyzer. If contamination is suspected, contact Roche Service.
r Examine the microwell plate after amplification and detection to ensure that no
leakage has occurred.
P To seal the microwell plate
1
Remove the protection layer from the sealing film.
Make sure not to touch the film neither on the adhesive side nor on the
non-adhesive side. Only touch the film at the removable edges.
2
Cover the microwell plate with the adhesive side of the sealing film.
3
Firmly press the sealing film to the plate surface using the sealing film applicator.
Q
To ensure a strong seal, use the provided sealing film applicator.
4
Remove both ends of the sealing film alongside the perforation.
Do not lift the sealing film from the plate while tearing off the ends of the film.
Figure 5 Sealing the microwell plate
S
Roche Diagnostics
16 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Operation cobas® 4800 System
Performing a run PIK3CA Mutation Test RUO
Starting amplification and detection run
The sealed microwell plate has to be inserted into the analyzer for amplification and
detection.
Limited stability of working
master mix
The prepared specimens added to working master mix have limited stability. Make
sure not to wait too long before starting the amplification and detection run.
U
For information about the exact timing window, refer to the test-specific package insert.
Xenon lamp replacement Before starting a run, check the Overview > System > cobas z 480 tab if the Xenon
lamp needs replacement. Replace the Xenon lamp, if required.
U
For details about Xenon lamp replacement, refer to the cobas z 480 analyzer Instrument
Manual.
P To load the prepared microwell plate into the analyzer
1
Press the load button on the analyzer.
Figure 6 Loading prepared microwell plate
The microwell plate loader opens.
2
Place the sealed microwell plate into the loading frame of the microwell plate
loader.
3
Press the load button again to close the microwell plate loader.
The microwell plate loader is retracted. The run starts immediately if the
microwell plate barcode matches the microwell plate barcode scanned in the
previous step.
NOTICE
Instrument damage due to improper handling
Do not turn off the analyzer power during a run.
When the run is finished, in the software, the Show result button becomes
available.
S
A Load button B Microwell plate loader
B
A
Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 17
cobas® 4800 System Operation
PIK3CA Mutation Test RUO Performing a run
Reviewing and accepting results
Test results are displayed in the Results work area.
P To review and accept results
1
In the Workplace work area, choose the Show result button.
Figure 7 Displaying results
The Results work area is displayed.
2
Review and accept results in the Results work area.
U
For details, see Accepting results (p. 24).
3
To print the results report, select results and choose (Print).
U
For details, see Printing results (p. 25).
S
Sending results to LIS
After review, test results can be sent to the LIS.
Q
o This step can be skipped if working without LIS.
o Results sent to LIS are kept in the Results work area. They are not deleted from the
results database.
P To send results to the LIS
1
To display the Results work area, choose the Results tab.
2
To send a complete run, select the run header of the run.
3
To send only certain results, select the results you want to send.
o To select several nonadjacent results, use the Ctrl key.
o To select a range of adjacent results, use the Shift key.
If necessary, the displayed runs can be filtered and sorted. Control results are
always uploaded to LIS.
A Show result button
A
Roche Diagnostics
18 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Operation cobas® 4800 System
Performing a run PIK3CA Mutation Test RUO
4
Choose the Send results to LIS button.
Depending on the LIS configuration, only accepted results or all results are sent to
the LIS.
After successfully sending results to the LIS, a status is displayed in the Result
sent column.
Figure 8 Confirmation from LIS
S
Unloading the analyzer
Unload the microwell plate as soon as practical after the run has finished to prevent
plate leakage and contamination of the analyzer.
CAUTION
Risk of burns due to hot surfaces
r Before removing the microwell plate from the microwell plate loader, wait for an
appropriate time to allow the microwell plate loader and microwell plate to cool down.
Be aware that the microwell plate may have a temperature of 60 °C to 80 °C even if you
have allowed the analyzer to cool down after the run. Otherwise, there is a risk of burns
when touching the microwell plate loader or microwell plate.
P To unload the analyzer
1
When the run has finished, open the microwell plate loader to remove the
microwell plate.
2
Examine the microwell plate after amplification and detection.
CAUTION
Incorrect results due to microwell plate leakage
Plate leakage can lead to incorrect results or can contaminate the analyzer. If
contamination is suspected, contact Roche Service.
r Unload the microwell plate as soon as practical after the run has finished and
check the microwell plate for indications of leakage.
3
Discard the plate according to the appropriate local regulations.
S
AResult sent column (must be selected in
the Column Chooser).
CSent means that LIS has not acknowledged
the results.
BConfirmed means that result was
successfully sent to LIS and LIS confirmed
the result. This will only be displayed if a
certain protocol is used by LIS.
D Failed means that the sending of results to
LIS failed.
B
A
D
C
Roche Diagnostics
cobas® 4800 System, Operator’s Manual RUO · Version 1.0 19
cobas® 4800 System Operation
PIK3CA Mutation Test RUO Sample editor
Performing shutdown procedure
To shut down the system, the following steps need to be performed.
P To shut down the system
1
Shut down the system in the following order:
o Switch off the analyzer.
o Choose (Exit), and switch off the control unit.
S
Sample editor
You can use the sample editor to prepare one or more work order files before starting
a run, or to prepare a work order file for the next run while a run is still in progress. A
work order file can be selected in the Select test dialog box.
The work order file is an XML-file that contains all orders for a single run on the
system. The work order file is loaded at the beginning of a run. For each run, the
information in the work order file must match the loaded samples on the system.
Messages in the sample editor If an error happens while creating a work order file, an error message is displayed.
Figure 9 Errors within the sample editor
A Message originating from an error in the Sample ID column
A
Roche Diagnostics
20 cobas® 4800 System, Operator’s Manual RUO · Version 1.0
Operation cobas® 4800 System
Sample editor PIK3CA Mutation Test RUO
Using the sample editor to create a work order file
Use the sample editor to create a work order file for the next run while a run is still in
progress. You can also use the sample editor to create one or more work order files
before starting a run.
P To create a work order file with the sample editor
1
In the global action bar, choose (Editor).
The Select test dialog box is displayed.
2
Select the PCR Only option.
3
Select the PIK3CA RUO check box.
4
Choose the OK button.
5
Create the work order file as described above.
U
For information on how to create a work order file, see To create a work order file for
microwell plate setup (p. 14).
S
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