Roche cobas 5800 User manual

cobas omni Utility Channel RUO

User Assistance Version 1.0

Utility Channel Tool software version 2.0

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

2

Publication information

Edition notice This publication is intended for operators of the

cobas omni Utility Channel.

Every effort has been made to ensure that all the

information contained in this publication is correct at the

time of publishing. However, the manufacturer of this

product may need to update the publication information

as output of product surveillance activities, leading to a

new version of this publication.

!

General attention

To avoid incorrect results, ensure that you are familiar

with the instructions and safety information.

r Pay particular attention to all safety notices.

r Always follow the instructions in this publication.

r Do not use the software in a way that is not described

in this publication.

r Store all publications in a safe and easily retrievable

place.

Training Do not carry out operation tasks or maintenance actions

unless you have received training from Roche

Diagnostics. Leave tasks that are not described in the

user documentation to trained Roche Service

representatives.

Screenshots The screenshots in this publication have been added

exclusively for illustration purposes. Configurable and

variable data, such as tests, results, or path names visible

therein must not be used for laboratory purposes.

Warranty Any customer modification to the system renders the

warranty or service agreement null and void.

For conditions of warranty, contact your local sales

representative or refer to your warranty contract partner.

Always leave software updates to a Roche Service

representative or perform such updates with their

assistance.

reserved.

Publication version Software version Revision date Change description

1.0 2.0 February 2017 First version

y Revision history

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

3

License information cobas omni Utility Channel Tool and cobas omni

Optimization Tool are protected by contract law, copyright

law, and international treaties.

cobas omni Utility Channel Tool and cobas omni

Optimization Tool contain a user license between F.

Hoffmann-La Roche Ltd. and a license holder, and only

authorized users may access the software and use it.

Unauthorized use and distribution may result in civil and

criminal penalties.

Open Source and Commercial Software cobas omni Utility Channel Tool and cobas omni

Optimization Tool may include components or modules of

commercial or open-source software. For further

information on the intellectual property and other

warnings, as well as licenses pertaining to the software

programs included in cobas omni Utility Channel Tool

and cobas omni Optimization Tool, refer to the

electronic distribution included with this product.

This open source and commercial software and

cobas omni Utility Channel Tool and cobas omni

Optimization Tool as a whole can constitute a device

regulated in accordance with applicable law. For more

detailed information, refer to the user manual and

labeling.

Please note that the respective authorization is no longer

valid according to the corresponding legislation should

any unauthorized changes be made to

cobas omni Utility Channel Tool and cobas omni

Optimization Tool.

Trademarks The following trademarks are acknowledged:

COBAS, COBAS OMNI, TAQMAN, AMPERASE, 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 publication

fulfills the intended use. All feedback on any aspect of

this publication is welcome and is considered during

updates. Contact your Roche representative, should you

have any such feedback.

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

4

Contact addresses

Roche Diagnostics GmbH

Sandhofer Strasse 116

68305 Mannheim

Germany

Made in Switzerland

Distributed in the US by:

Roche Diagnostics

9115 Hague Road

Indianapolis

Indiana

USA

Table of contents 5

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

Table of contents

Publication information 2

Contact addresses 4

Table of contents 5

Intended use 7

Symbols and abbreviations 7

Safety classifications 8

Safety information 10

Operation

1Operation

Workflows 15

Utility channel software 17

RFID reader/writer 28

Installing a UC analysis package onto the

system 31

Preparing the reagent cassette 36

Performing and viewing tests 43

Optimization software

2 Optimization software

About the optimization software 49

About the optimization software user

interface 50

Workflows 52

Using the optimization software 54

Appendix

3 Utility channel test guidelines

Recommendations for test design 71

Disclaimer 72

Primer and probe 73

PCR profile 77

Controls 79

Optimizing a qualitative real time PCR test 80

References 88

Attachment 1: Examples for PCR profiles 89

Attachment 2: Primer design software

programs available on the Internet 90

4 Installing the software

Installing the utility channel software 93

Installing the optimization software 96

Index

Index 101

6 Table of contents

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

7

Intended use

The cobas omni Utility Channel suite of products utilizes

the open channel functionality of the cobas

®

6800/8800

Systems Software in order to support the development

and routine performance of user-defined real-time PCR

tests on the cobas

®

6800/8800 Systems.

The cobas omni Utility Channel is intended for research

use only and is not for use in diagnostic procedures.

Symbols and abbreviations

Product names Except where the context clearly indicates otherwise, the

following product names and abbreviations are used:

Symbols used in the publication

Product name Abbreviation

cobas

®

6800/8800 Systems

system

cobas

®

Buffer Negative Control

Kit

negative control

cobas omni Optimization Kit optimization kit

cobas omni Utility Channel Tool utility channel software

cobas omni Utility Channel

Reagent Kit

reagent kit

cobas omni Utility Channel

Master Mix Reagent 2

master mix reagent 2

cobas omni Optimization Tool optimization software

Master Mix Reagent 1 master mix reagent 1

y Product names

Symbol Explanation

o List item

u Related topics containing further information

q

Tip. Extra information on correct use or useful

hints.

r Start of a task

I Extra information within a task

f Result of an action within a task.

c Frequency of a task.

n Duration of a task.

d Materials that are required for a task.

j Prerequisites of a task.

u Topic. Used in cross-references to topics.

p Task. Used in cross-references to tasks.

w

Figure. Used in figure titles and cross-

references to figures.

y Symbols used in the publication

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

8

Abbreviations The following abbreviations are used.

Safety classifications

The safety precautions and important user notes are

classified according to the ANSI Z535.6-2011 standard.

Familiarize yourself with the following meanings and

icons:

!

Safety alert

r The safety alert symbol is used to alert you to potential

physical injury hazards. Obey all safety messages that

follow this symbol to avoid possible damage to the

system, injury, or death.

These symbols and signal words are used for specific

hazards:

WARNING

!

Warning...

r ...indicates a hazardous situation which, if not avoided,

could result in death or serious injury.

y

Table. Used in table titles and cross-references

to tables.

z

Equation. Used in cross-references to

equations.

k

Code example. Used in code titles and cross-

references to codes.

Symbol Explanation

y Symbols used in the publication

Abbreviation Definition

ANSI American National Standards

Institute

CSA Canadian Standards Association

EC European Community

IVD in-vitro diagnostic

RUO Research Use Only

TCP Transmission Control Protocol

UL Underwriters Laboratories Inc.

y Abbreviations

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

9

CAUTION

!

Caution...

r ...indicates a hazardous situation which, if not avoided,

could result in minor or moderate injury.

NOTICE

Notice...

...indicates a hazardous situation which, if not avoided,

may result in damage to the system.

Important information which is not safety relevant, is

indicated with the following icon:

q Tip...

...indicates additional information on correct use or useful

tips.

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

10 Safety information

Safety information

Data loss or unavailability of the system due

to malicious software or unauthorized system

access

Malicious software or unauthorized system access can

result in data loss or system unavailability.

To avoid infection of malicious software or the misuse of

the system, the following recommendations are essential:

r Customers are responsible for the security of their

local area network, especially in protecting it against

malicious software and attacks. This protection

includes a firewall, to separate the device from

uncontrolled networks, as well as measures that

ensure that the connected network is free of malicious

code.

r Make sure that any necessary third-party software is

kept up-to-date.

r Use an appropriate and up-to-date anti-virus and

anti-malware software on the PC where the utility

channel software is running.

r Enable the Data Execution Prevention (Windows

security feature) on the client system for the utility

channel software.

r Do not connect any untrusted external storage

devices (such as USB flash drives or external hard

drives) to the system.

Skin inflammation or injury Direct contact with reagents, detergents, cleaning

solutions, or other working solutions may cause skin

irritation, inflammation, or burns.

r When you handle reagents, exercise the precautions

required for handling reagents.

r Wear appropriate personal protective equipment.

r Observe the instructions given in the Instructions for

Use.

r Observe the information given in Material Safety Data

Sheets (available for Roche Diagnostics reagents and

cleaning solutions).

r If reagents, detergents, or other cleaning solutions

come into contact with your skin, wash the affected

area immediately with soap and water and apply a

disinfectant.

Consult a physician.

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

Operation

1 Operation

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

13

Table of contents

Operation 1

In this chapter

1

Workflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Test development workflow . . . . . . . . . . . . . . . . . . 15

Routine workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Utility channel software . . . . . . . . . . . . . . . . . . . . . . . . . 17

Compatible system software. . . . . . . . . . . . . . . . . . 17

About the user interface . . . . . . . . . . . . . . . . . . . . . 18

Creating an unpublished UC analysis package . . 18

Opening an unpublished UC analysis package . . 19

Defining and editing a UC analysis package . . . . 21

Publishing a UC analysis package . . . . . . . . . . . . . 24

Creating a new package from a published UC

analysis package . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Opening a published UC analysis package to

write to a reagent cassette RFID tag . . . . . . . . . . . 26

RFID reader/writer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

About the RFID reader/writer . . . . . . . . . . . . . . . . . 28

Reading and writing on an RFID tag . . . . . . . . . . . 28

Installing a UC analysis package onto the system. . . 31

Importing and installing a UC analysis package

onto the system via remote connection . . . . . . . . 31

Uninstalling a UC analysis package from the

system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Reinstalling a UC analysis package onto the

system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Preparing the reagent cassette . . . . . . . . . . . . . . . . . . 36

About the reagent kit. . . . . . . . . . . . . . . . . . . . . . . . 36

Preparing the master mix reagent 2. . . . . . . . . . . . 37

Filling the reagent cassette . . . . . . . . . . . . . . . . . . . 38

Quick reference: Preparing the reagent cassette 41

Performing and viewing tests . . . . . . . . . . . . . . . . . . . . 43

Performing a utility channel test. . . . . . . . . . . . . . . 43

About viewing test results. . . . . . . . . . . . . . . . . . . . 44

1 Operation

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

14

Table of contents

1 Operation

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

Operation 15

Workflows

In this section

Test development workflow (15)

Routine workflow (16)

Test development workflow

u Related topics

• Optimization software (47)

Utility channel software RFID reader/writer Reagent cassette

cobas

®

6800/8800

Systems

1

Create analysis

package

2 Write reagent

cassette ID and lot

No. to RFID tag

3 Install analysis

package to analytic

system

4 Prepare reagent

cassette and load

onto analytic

system

5 Perform test

6 Receive test results

1 Operation

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

16 Workflows

Routine workflow

For use when the UC analysis package is already installed

on the system.

u Related topics

• Optimization software (47)

Utility channel software RFID reader/writer Reagent cassette

cobas

®

6800/8800

Systems

1

Open published

analysis package

2 Write reagent

cassette ID and

lot No. to RFID tag

3 Prepare reagent

cassette and load

onto the analytic

system

4 Select installed

UC test on

analytic system

5 Perform test

6 Receive test

results

1 Operation

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

Operation 17

Utility channel software

In this section

Compatible system software (17)

About the user interface (18)

Creating an unpublished UC analysis package (18)

Opening an unpublished UC analysis package (19)

Defining and editing a UC analysis package (21)

Publishing a UC analysis package (24)

Creating a new package from a published UC analysis

package (25)

Opening a published UC analysis package to write to a

reagent cassette RFID tag (26)

Compatible system software

The following table lists the compatible versions of the

system software, the utility channel software, and the

optimization software.

q Only UC analysis packages created in a compatible

version of the utility channel software can be used and

loaded onto the system.

u Related topics

• Optimization software (47)

• Installing the software (91)

Utility channel software version Optimization software version cobas

®

6800/8800 Systems software version

2.0 2.0 1.02.12

y Compatible software versions

1 Operation

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

18 Utility channel software

About the user interface

The utility channel software user interface follows the

same design concept as the cobas

®

6800/8800 Systems.

The user interface is highly simplified and consists of only

5 panels. The panels are described in the following table:

Creating an unpublished UC analysis package

Follow this procedure to set up a new unpublished UC

analysis package.

UC analysis package A UC analysis package is a bundle of files that contain

parameters and specifications relevant for a specific test.

It provides the test definition for the robotics, calculation

packages for the result calculation, and libraries for the

plausibility calculation.

You can either create a UC analysis package from a

template or from an existing published package.

Naming Ensure that each UC analysis package has a unique name

(e.g., by adding a version to the name). It is not possible

to install analysis packages with the same name onto the

system.

Panel Description

Utility channel tool User interface home panel. The Utility channel tool panel includes a list of recently used UC analysis

packages. You can open an analysis package by choosing the icon in the list. Open an unpublished

analysis package to continue editing or open a published analysis package to write on the RFID tag.

The Utility channel tool panel also includes the following task buttons:

o Create UC analysis package from template

o Create from published UC analysis package

o Open unpublished UC analysis package

o Open published UC analysis package to write on reagent cassette RFID tag

UC analysis package The UC analysis package panel is displayed when you create or open a UC analysis package. You

can define or edit analysis package information in the following fields:

o UC analysis package name

o Reagent cassette ID

Further package definition is available by choosing the PCR profile, Parameter, and Reagent

cassette buttons. When complete, you can save or publish the package by choosing the Publish,

Save as, or Save buttons at the bottom of the panel.

PCR profile The PCR profile detail panel is displayed when you choose the PCR profile button on the UC

analysis package panel. This panel allows you to define the number of steps, temperature, and hold

time during the pre-PCR, first measurement, and second measurement phases of PCR.

Parameter The Parameter detail panel is displayed when you choose the Parameter button on the UC analysis

package panel. This panel allows you to define the sample volume, number of channels (including

target name and sensitivity), and an optional internal control validation. If selected, the internal control

validation includes definitions for positive target confirmation with or without IC, lower and upper Ct

limits, and sensitivity.

Reagent cassette The Reagent cassette detail panel is displayed when you choose the Reagent cassette button on

the UC analysis package panel. This panel allows you to read data from, or write data on, an RFID

tag.

y Description of the user interface panels

1 Operation

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

Operation 19

r To create an unpublished UC analysis

package

1

On the Utility channel tool panel, do one of the

following:

• Choose the Create UC analysis package from

template button.

• Choose the Create from published UC analysis

package button. On the Open dialog box,

navigate to the package to be opened and choose

the Open button.

I Published UC analysis packages to be opened

must be .ZIP files.

2

On the UC analysis package panel, fill in the UC

analysis package name field, and the Reagent

cassette ID field.

I Entries for the UC analysis package name field

and the Reagent cassette ID field must begin

with the prefix "U_".

3

Save the UC analysis package as follows:

• Choose either the Save as button or the Save

button.

• Navigate to where you want to save the UC

analysis package, enter the file name, and choose

the Save button.

I Unpublished UC analysis packages are stored as

.UDF files.

u Related topics

• Defining and editing a UC analysis package (21)

Opening an unpublished UC analysis package

Follow this procedure to open an unpublished UC

analysis package.

q The file to be opened must be a .UDF file.

d m UC analysis package

1

2

1 Operation

Roche Diagnostics

cobas omni Utility Channel RUO · Utility Channel Tool software version 2.0 · User Assistance · Version 1.0

20 Utility channel software

r To open an unpublished UC analysis

package

1

On the Utility channel tool panel, choose the Open

unpublished UC analysis package button.

2

On the Open dialog box, navigate to the package to

be opened and choose the Open button.

I The file to be opened must be a .UDF file.

3

The utility channel software maintains shortcuts for

recently used UC analysis packages. To open a UC

analysis package, at the bottom of the Utility channel

tool panel, choose the shortcut.

4

Save the UC analysis package as follows:

• Choose either the Save as button or the Save

button.

• Navigate to where you want to save the UC

analysis package, enter the file name, and choose

the Save button.

u Related topics

• Defining and editing a UC analysis package (21)

1

2

3

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