Roche cobas z 480 User manual

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.

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.

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.

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.

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).

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

Manually prepare

reagents and samples

Start new run

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.

For a complete and detailed description of the workflow, see Operation (p. 10).

Step User action

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.

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.

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.

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

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.

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.

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.

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

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

P To start up and log on to the software

Switch on the monitor and control unit.

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.

Enter your assigned user ID and password.

Choose the OK button.

o The user ID is not case sensitive.

o The password is case sensitive. The password displays as asterisks when typed to

maintain security.

P To manually prepare the reagents and specimens

Remove the reagents and specimens from storage.

For information on handling and preparing reagents and specimens, refer to the

test-specific package insert.

Manually prepare the reagents and specimens according to the instructions in the

test-specific package insert.

A Power switch of the analyzer

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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.

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.

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.

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

Choose (New run).

The Select test dialog box is displayed.

Figure 3 Select test dialog box

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

Select the PIK3CA RUO check box.

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").

Choose the OK button.

The Workplace tab is displayed showing the wizard for the new run.

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

Roche Diagnostics

14 cobas® 4800 System, Operator’s Manual RUO · Version 1.0

Operation cobas® 4800 System

Performing a run PIK3CA Mutation Test RUO

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

Scan the microwell plate barcode into the Microwell Plate ID field.

Scan the barcode of the DNA sample preparation kit into the first field of the

DNA Sample Preparation Kit-ID column.

Scan the barcode of the cobas® PIK3CA Mutation Test kit into the first field of the

PIK3CA Mutation Test Kit-ID column.

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).

Scan the sample ID barcodes into the Sample ID column in the lower part of the

screen.

For information about the pipetting order, refer to the test-specific package insert.

If you use more than one test kit, repeat steps 2 to 5 for each test kit in the order

described above.

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.

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.

Choose the Next button.

P To pipette the reagents and prepared specimens into the microwell plate

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.

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

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.

Cover the microwell plate with the adhesive side of the sealing film.

Firmly press the sealing film to the plate surface using the sealing film applicator.

To ensure a strong seal, use the provided sealing film applicator.

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

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.

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.

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

Press the load button on the analyzer.

Figure 6 Loading prepared microwell plate

The microwell plate loader opens.

Place the sealed microwell plate into the loading frame of the microwell plate

loader.

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.

A Load button B Microwell plate loader

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

In the Workplace work area, choose the Show result button.

Figure 7 Displaying results

The Results work area is displayed.

Review and accept results in the Results work area.

For details, see Accepting results (p. 24).

To print the results report, select results and choose (Print).

For details, see Printing results (p. 25).

Sending results to LIS

After review, test results can be sent to the LIS.

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

To display the Results work area, choose the Results tab.

To send a complete run, select the run header of the run.

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

Roche Diagnostics

18 cobas® 4800 System, Operator’s Manual RUO · Version 1.0

Operation cobas® 4800 System

Performing a run PIK3CA Mutation Test RUO

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

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

When the run has finished, open the microwell plate loader to remove the

microwell plate.

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.

Discard the plate according to the appropriate local regulations.

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.

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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

Shut down the system in the following order:

o Switch off the analyzer.

o Choose (Exit), and switch off the control unit.

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

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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

In the global action bar, choose (Editor).

The Select test dialog box is displayed.

Select the PCR Only option.

Select the PIK3CA RUO check box.

Choose the OK button.

Create the work order file as described above.

For information on how to create a work order file, see To create a work order file for

microwell plate setup (p. 14).

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