System Manual Software Version 2 - · PDF filecobas® 4800 System Document information Systeni Manual Revision history Instrument approvals Roche Diagnostics 2 Manual version Software

cobas® 4800 SystemSystem ManualSoftware Version 2.1

cobas® 4800 System

Document information

Systeni Manual

Revision history

Instrument approvals

Roche Diagnostics

2

Manual version Software version Revision date Changes

1.0 2.1 April2013

Table 1 Revsion history

Edition notice This manual is for users of the cobas 4800 System.

Every effort has been made to ensure that all the information contained in thismanual is correct at the time of printing. However, Roche reserves the right to makeany changes necessary without notice as part of ongoing product development.

Any customer modification to the cobas x 480 instrument or cobas z 480 analyzerwill render the warranty or service agreement null and void.

Software updates are done by Roche Service representatives.

The screenshots in this publication have been added exclusively for the purpose ofilustration. Configurable and variable data such as parameters, resuits, path namesetc. visible therein must not be used for laboratory purposes.

Intended use The system is intended to be used as a diagnostic or screening system providingsamplepreparation, amplification and detection of specific targets from humansamples.

It is important that the operator reads this manual and the test-specific Operator’sManual thoroughly before using the system.

The system is to be used by laboratory professionals trained in laboratory techniquesand by instruction on the use of the system.

Copyright © 2013, Roche Diagnostics International Ltd. All rights reserved.

Tradernarks 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 fulfills the intended purpose asmentioned above. All feedback on any aspect of this manual is welcome and will beconsidered during updates. Please contact your Roche representative, should youhave any such feedback.

The instrument and the analyzer meet the protection requirements laid down in IVDDirective 98/79/EG.

Furthermore, the analyzer is manufactured and tested according to the followinginternational standards:

• lEG 61010-1

• lEG 61010-2-101

• UL61O1O-1

• CAN/CSA C22.2 No. 61010-1

This manual meets the European Standard EN ISO 18113-3.

Compliance is demonstrated by the following marks:

System Manual . Version 1.0

cobas® 4800 System

Systeni Manual

Contact addresses

Roche Diagnostics


C ( Complies with the IVD directive 98/79/EG.

Issued by underwriters laboratories, mc. (UL) for Canada and the US.

C®(JS

Roche Molecular Systems, mc.1080 U.S. Highway SouthBranchburg, NJ 08876- 1760USAMade in Switzerland

Roche Diagnostics GmbH1 ECIREPI SandhoferStrasse 11668305 MannheimGermany

3

cobas® 4800 System

System Manual

Roche Diagnostics

4 System Manual Version 1.0

cobas® 4800 System

Sys(em Iftinunl

Table of contents

Document informationContact addressesTable of contentsPrefaceHow to use this manualWhere to find informationConventions used in this manual

4 Software

Basic software elementsDatabase

Configuration

73

81

5 Configuration

Configuration 87User management 92Exporting support data 97Result counters 98

Maintenance

6 Maintenance

Safety informationInstrument maintenanceAnalvzer maintenance

Roche Diagnostics


103104

115

Troubleshooting7

357

777

System description

7 Troubleshooting

Overview 129Messages work area 131About result flags 134General troubleshooting 136Hardware troubleshooting 138

Glossary

8 Glossary

Index

Index 149

Revisions

1 General safety information

Safety classificationsSafety precautionsSafety summarySafety labels on the systemDisposal

2 Overview

System overview

3 Hardware

InstrumentAnalyzerControl unit

1516182527

31

396569

5

cobas® 4800 System

System I’4anual

Roche Diagnostics

System Manual Version 1.06

cobas® 4800 System

Systeni Manual

Preface

The system integrates fully automated total nucleic acid isolation directly fromprimary and secondary tubes, automated PCR setup, and real time PCR.

This manual covers the complete system comprised of the cobas’ 4800 software, theinstrument used for sample preparation, and the analyzer used for amplification anddetection using real time PCR.

How to use this manual

• Keep this manual in a safe place to ensure that t is not damaged and remains available

for use.

• This manual should be easily accessible at all times.

To help you find information quickly, there is a table of contents at the beginning ofthe manual and each chapter. In addition, a complete index can be found at the endof the manual.

Where to find information

In addition to this manual, the following documents are also provided to assist infinding desired information quickly:

Test-specfic Operator Manuals For each test, there is a specific Operator’s Manual which describes how to prepareand perform a run, and how to handle results.

Test-specficpackage insert For each test, there is a package insert which provides additional information. Forexample, instructions on storage and handling of reagents, samples and controls.

Conventions used in this manual

Visual cues are used to help locate and interpret information in this manual quickly.This section explains formatting conventions used in this manual.

Symbols The following symbols are used:

Symbol Used for

( Start of procedure

End of procedure

List item

(j) Cross-reference

C’ Cail-up (software reference)

Table 2 Symbols used

Roche Diagnostics

System Manual Version 1.0 7

cobas® 4800 System

Systern Manual

Symbol Used for

J Tip

j/’ Safety alert

‘.‘ Electrical and electronic equipment marked with this symbol are/Y\ covered by the European Directive 2002/961EC on waste electrical

and electronic equipment (WEEE).

The symbol denotes that the equipment must not be disposed of inthe municipal waste system.

Table 2 Symbols used

Abbreviations The following abbreviations are used:

Abbreviation Definition

AD Amplification and detection

ANSI American National Standards Institute

cc cubic centimeter

cLLD Capacitive Liquid Level Detection

CSA Canadian Standards Association

dBA decibel weighted against the A-frequency response curve. This curveapproximates the audible range of the human ear.

DIL Diluent

DWP Deepweil Plate

EC European community

e.g. exempli gratia — for example

EMC ElectroMagnetic Compatibility

EN European standard

ie. id est — that is to say

IEC International Electrical Commission

iSWAP internal Swivel Arm Plate handler

IVD In Vitro Diagnostic

KVA kilovolt-Ampere

LED Light Emitting Diode

LIS Laboratory information system

MWP Microweli plate

n/a not applicable

PCR Polymerase Chain Reaction

QC Quality Control

SD Standard deviation

UL Underwriters Laboratories mc.

UPS Uninterruptible Power Supply

WEEE Waste Electrical and Electronic Equipment

XML Extensible Markup Language

Table 3 Abbreviations

Roche Diagnostics

8

Product narnes The following product names are used:


cobas® 4800 System

Systern Manual

Roche Diagnostics


Product name Abbreviation

cobas 4800 software software

cobas x 480 instrument instrument

cobas z 480 analyzer analyzer

cobas 4800 System system

Tahie 4 Product nam es

9

cobas® 4800 System

Systeni Manual

Roche Diagnosti


System description

1 General safety information 13

2 Overview 29

3 Hardware 37

4 Software 71

cobas® 4800 System 1 General safety information

Table of contents Systern Manual

General safety information

In this chapter, you will find information on the safe operation of the system.

In this chapter Chapter

Safety classifications 15

Safety precautions 16

Operator qualification 16

Safe and proper use of the system 16

Miscellaneous safety precautions 17

Safety summary 18

Warning messages 18

Electrical safety 18

Optical safety 18

Biohazardous materials 19

Waste 19

Explosion and fire risk 20

Caution messages 20

Mechanical safety 20

Reagents and consumables 21

Interfering substances in samples 21

Evaporation of samples or reagents 21

Incorrect resuits due to two barcode labels or incorrect specimen labeling....22

Incorrect resuits due to wrongly typed sample IDs 22

Carryover 22

Hot surfaces 22

Malfunction due to interfering electromagnetic fields 22

Data security 23

Notices 23

Movingparts 23

Circuit breakers and fuses 24

Spilage 24

Safety labels on the system 25

Safety labels on the instrument 25

Safety labels on the analyzer 26

Roche Diagnostics

System Manual . Verson 1.0 13

1 General safety information cobas® 4800 System

Table of contents System Manual

Disposal 27

Disposal of the instrument 27

Disposal of the analyzer 27

Disposal of control unit components 27

Roche fliagnostics

14 System Manual . Version 1.0


Systern Manual Safety c1assfications

Safety classifications

This section explains how precautionary information is presented in this manual.

The safety precautions and important user notes are classified according to theANSI Z535.6 Standard. Famiiarize yourselfwith the following meanings and icons:

Safety information

The safety alert symbol by itself without a signal word is used to promote awareness tohazards which are generic or to direct the reader to safety information providedelsewhere in the document.

These symbols and signal words are used for specific hazards:

WARNING

1 Indicates a hazardous situation which, if not avoided, could result in death or serious

WARNING Injury.

CAUTION

Indicates a hazardous situation which, if not avoided, could result in minor or moderate

CAUTION injury

NOTICE NOTICE

lndicates a hazardous situation which, if not avoided, could result in damage toequipment.

For more information about product safety labels, see Safety labels on the systern (p. 25)

Important information which is not safety relevant is indicated by the followingsymbol:

Tip

Indicates additional information on correct use of the system or useful tips.

Roche Diagnostics

System Manual . Version 1.0 15


Safetyprecautions System Manual

Safety precautions

Safety information

Particular attention must be paid to the following safety precautions. 1f these safety

precautions are ignored, the operator may suffer serious or fatal injury. Each

precaution is important.

Operator qualification

Operators are required to have a sound knowledge of relevant guidelines andstandards as well as the information and procedures contained in all relevantmanuals.

• Do not carry out operation and maintenance unless you have been trained byRoche Diagnostics.

• Carefully follow the procedures specified in all relevant manuals for operationand maintenance.

• Leave maintenance, installation, or service that is not described in the manuals totrained Roche Service personnel.

• Follow standard laboratory practices, especially when working with biohazardousmaterial.

Safe and proper use of the system

Personal protective equipnient • Be sure to wear appropriate protective equipment, including, but not limited to,safety glasses with side shields, fluid resistant lab coat, and approved disposablegloves.

• Wear a face shield ifthere is a chance of splash or splatter.

Accuracy/precision of measured • Do not use reagents that have exceeded their expiry date, otherwise inaccurateresults data may be obtained.

• For diagnostic purposes always assess the resuits in conjunction with the patient’smedical history, clinical examination, and other findings.

• Each laboratory must verify that reagent performance meets the publishedspecifications.

.Installation • Unpacking and installation must be performed by trained Roche Servicepersonnel only.

• Leave installation that is not described in this manual or the test-specificOperator’s Manuals to trained Roche Service personnel.

Correct use • Use the instrument only for preparing liquid samples with the provided reagents.

Operating conditions • Operation outside of the specified ranges, e.g. with excessive environmentaltemperature and/or humidity, may lead to incorrect resuits or malfunction of theinstrument or analyzer.

• Use the instrument and analyzer as indicated in the technical specifications.

• Make sure that the instrument’s and analyzer’s ventilation openings remainunobstructed at all times.

Roche Diagnostics



Systern Manual Safetyprecautions

• Perform maintenance according to the specified intervals to maintain theoperating conditions of the instrument and analyzer.

• Keep all manuals in a safe place to ensure that it is not damaged and remainsavailable for use. All manuals must be easily accessible at all times.

Approvedparts Use of non-approved parts or devices may result in malfunction of the instrument oranalyzer and may render the warranty nuli and void. Only use parts and devicesapproved by Roche Diagnostics.

Third-party software Installation of any third-party software that is not approved by Roche Diagnosticsmay result in incorrect behavior of the system or the software. Do not instali anynon-approved software.

Miscellaneous safety precautions

Power interruption A power failure or momentary drop in voltage may lead to data loss. Operation withan uninterruptible power supply (UPS) is strongly recommended. Check the UPSregularly to make sure it functions properly.

1f there is a power failure, the analyzer is disconnected from the control unit. Thedisplayed maintenance status of the analyzer may not be correct. To get the correctmaintenance status, refresh the analyzer under Overview> System > cobas z480 tab.

Electrornagneticfields Devices that emit electromagnetic waves may cause the instrument or analyzer tomalfunction. Do not operate the following devices in the same room where theinstrument or analyzer are installed:

• Mobile phone

• Transceiver

• Cordless phone

• Other electrical devices that generate electromagnetic fields

Data backup There is an automatic backup process that stores the data on the D drive. It is thecustomers responsibility to perform regular backups of all measurement results.

Relocation and transportation Do not attempt to relocate or transport the instrument or analyzer. Leave relocationand transportation to personnel trained or authorized by Roche.

For additional details, see Disposal (p. 27)

Roche Diagnostics



Safety surnmay Systeni Aianual

Safety summary

This safety summary contains the most important and general warning and cautionmessages. Additionally, you will find specific safety information at the beginning ofPart Ivfaintenance (p. 101) and in the test-specific Operator’s Manuals.

For more information about the safe use of the system, refer to the test-specific packageinsert.

Warning messages

List of warning messages

Before operating the system, read the warning messages contained in this summary

WARNING and in all relevant manuals carefully. Failure to observe them may result in death or

serious injury

Electrical safety

Electrical shock by electronic equipment

Do not attempt to work in any electronic compartment.

WARNING Do not remove any cover of the instrument or analyzer other than those specified in

this manual or the test-specific Operators Manual.

Do not touch any parts of the instrument or analyzer other than those specified.

Especially do not touch any power supply parts.

Never remove the middle grounding prong from the power cable or defeat its purpose

by using an ungrounded adapter.

Installation, service, and repair must only be performed by personnel authorized and

qualified by Roche.

Observe the system safety labels as illustrated in section Safety labels on the system

(p25)

Optical safety

Loss of sight due to stanng into laser beam

The barcode reader on the autoloader of the instrument contains a class II laser diode.

WARNING Do not stare into the laser transmitter beam as eyesight may be severely damaged.

Roche Diagnostics



System j’vlanual Safrty summary

Biohazardous materials

Infection by samples and associated matenals

Contact with samples containing material of human origin may result in infection. All

WARNING materials and mechanical components associated with samples of human origin are

potentially biohazardous. Therefore, universal precautions should be taken when handling

and processing samples.

Follow standard laboratory practices, especially when working with biohazardous

material.

Keep the main cover closed and in place while the instrument is operating.

Do not open the thermal block cycler door during operation.

When working with the main cover open while the instrument is powered on (eg., for

cleaning or maintenancej, always put the instrument in Maintenance mode or in

Shutdown status first.

Be sure to wear appropriate protective equipment, including, but not limited to, safety

glasses with side shields, fluid resistant lab coat, and approved disposable gloves.

Wear a face shield if there is a chance of splash or splatter.

1f any biohazardous material is spilled, wipe it up immediately and apply disinfectant.

It sample or liquid waste comes into contact with your skin, wash it oft immediately

with soap and water, and apply a disinfectant. Consult a physician.

Infection and injury due to sharp objects

When wiping sharp objects, use several layers of gauze.

WARNING Be careful to not puncture yourself.

Be sure to wear appropriate protective equipment, for example gloves.

Waste

Infection by biohazardous waste

Liquid and solid waste originates from samples collected in media that inactivate

WARNING potentially biohazardous material. However, as with all human-derived solutions, universal

precautions should be taken when handling waste.

Contact with liquid waste or used pipetting tips may result in infection. All materials and

mechanical components that come into contact with waste are potentially biohazardous.

Therefore, universal precautions should be taken when handling waste.

Be sure to wear protective equipment. Take extra care when working with protective

gloves; these can easily be pierced or cut which can lead to infection.

1f any biohazardous material is spilled, wipe t up immediately and apply disinfectant.

1f liquid waste comes into contact with your skin, wash it off immediately with soap and

water, and apply a disinfectant. Consult a physician immediately

Observe the system safety labels as illustrated in section Safety labels on the system

(p.25)

Contamination of the environment by liquid waste and solid waste

The waste generated during the procedure is potentially biohazardous.

WARNING When disposing of any Jiquid or solid waste, do so according to the appropriate local

regulations.

For information about disposal, see Disposal (p. 27)

Roche Diagnostics



Safety surnniary Systeni Manual

Explosion and fire risk

Explosion through sparks

Hazard of explosion through sparks.

WARNING Keep all potentially flammable or explosive material (eg. anesthetic gas) away from the

instrument or analyzer.

Fire risk through usage of sprays

Spraying liquid on the power supply paas can cause a sho circuit and result in a fire.

WARNING During fire-fighting operations disconnect the equipment from the main power supply.

Keep the cover closed while the instrument and analyzer is connected to the main

power supply, and do not use sprays in the vicinity of the instrument and analyzer.

Caution messages

List of caution messages

Before operating the system, read the caution messages contained in this summa

CAUTION and in all relevant manuals carefully. Failure to observe them may result in minor or

moderate injury.

Mechanical safety

Personal injury due to contact with moving parts

The pipetting head of the instrument moves rapidly during sample preparation. The main

CAUTION cover is locked during operation, protecting the user from moving parts.


When working with the main cover open while the instrument is powered on (eg., for

cleaning or maintenance), always put the instrument in Maintenance mode or in

Shutdown status first.

Do not touch any parts of the instrument or analyzer other than these specified. Keep

away from moving parts during instrument operation.

Do not remove any carrier from the instrument deck while the instrument is operating.


During operation and maintenance of the instrument, proceed according to the

instructions.

Observe the system safety labels as illustrated in section Safety labels on the system(p. 25)

Roche Diagnostics



System Aianual Safety suniniary

Reagents and consumables

Skin infiammation or injury caused by reagents

Direct contact with reagents, detergents, or cleaning solutions may cause skin irritation,

CAUTION inflammation, or burns.

When handling reagents, exercise the precautions required for handling laboratory

reagents. Be sure to wear protective equipment (such as goggies, gloves).

Observe the cautions given in the package insert and observe the information given in

the Material Safety Data Sheets available for Roche Diagnostics reagents and cleaning

solutions.

b 1f a reagent or detergent comes into contact with your skin, wash t off immediately

with soap and water, and apply a disinfectant. Consult a physician immediately

Invalid results due to incorrect reagent volume

Incorrect reagent handling may cause an undetectable loss of reagent.

CAUTION Store reagents always according to specified storage conditions.

Do not leave opened sample containers on the system for any considerable Iength of

time to avoid evaporation.

Avoid creating foam 0fl top of reagents in filled reagent reservoirs and in reagent vials

that are placed on reagent carriers.

Partially used reagents should not be used on other cobas® 4800 systems.

Invalid results due to expired reagents and consumables

Data obtained using expired reagents and consumables are not reliable. Reagents are

CAUTION supplied in a kit package with a label that indicates the expiry date. The expiry date of

microwell plate and sealing film is printed on their package label.

Do not use reagents and consumables that have exceeded their expiry dates. Replace

expired reagents and consumables with unexpired reagents and consumables before

sample processing.

Choosing the wrong test kit

Make sure to choose the correct test kit for the required test. Choosing a wrong test kit

CAUTION will not let you proceed with the test.

Interfering substances in samples

Invalid resuits due to interfering substances

lnterfering substances in samples may cause clogging and lead to incorrect results.

CAUTION

Evaporation of samples or reagents

Pipetting errors due to evaporation of samples or reagents

Evaporation of samples or reagents may lead to pipetting errors.

CAUTION Do not leave opened sample containers on the system for any considerable length of

time.

For additional details, refer to test-specific package insert.

Processing of the samples must commence within specified time after reagent

barcodes have been scanned as indicated in the software.

Do not use expired reagents.

Roche Diagnostics



Safety sunimary Systeni Ivianual

Incorrect resuits due to two barcode labels or incorrect specimen labeling

Incorrect resuits due to two barcodes on the same tube or mixing up specimenbarcodes

CAUTION Duplicate barcodes are not accepted on the system within the same run.

Take adequate measures to avoid placing incorrect barcode on specimen.

Make sure that there is only one barcode on each specimen tube.

Incorrect resuits due to wrongly typed sample lOs

Incorrect resuits due to incorrect sample IDs

1f the sample IDs are entered manually, there is the risk of making spelling mistakes or

CAUTION entering wrong sample IDs.

After printing the microwell plate layout, compare the sample IDs on the tubes with thesample IDs on the microwell plate Iayout.

1f you notice a mistake, correct the mistake in the sample ID column. Then save the

work order file and use the new printout for setting up the microwell plate.

Carryover

Incorrect resuits due to carryover

Traces of analytes or reagents may be carried over from one test to the next.

Take adequate measures to prevent carryover and to avoid potentially false results.

When any indication of potential sources of contamiriation is seen (e.g. puncturedsealing film, spilled reagents or samples, etc.), or if manual sample preparation was notperformed according to good laboratory practice, proper decontamination procedures

must be performed.

Hot surfaces

Personal injury due to hot surface

The heater/shaker cradle on the instrument and the microwell plate holder, the thermalblock cycler, the block cycler cover, and the Xenon lamp on the analyzer are hot whileoperating.

Do not touch hot surfaces.

Malfunction due to interfering electromagnetic fields

Malfunction of system and incorrect results due to interfering electromagneticfields

Devices that emit electromagnetic waves may cause the analyzer to malfunction.

The electromagnetic environment should be evaluated prior to operation of the device.

Do not operate this system in close proximity to sources of strong electromagneticfields (for example unshielded intentional RF sources), as they may interfere withproper operations.

Roche Diagnostics



Systeni Manual Safety sunirnary

Data security

Unauthorized access and data loss due to malicious software and hacker attacks

Portable storage media can be infected with and transmit computer malware, which may

CAUTION be used to gain unauthorized access to data or cause unwanted changes to software.

The system is not protected against malicious software and hacker attacks.

The customers are responsible for IT security of their IT infrastructure and for protecting it

against malicious software and hacker attacks. Failure to do so may result in data loss or

render the system unusable.

Roche recommends the following precautions:

Allow connection to authorized external devices only

Ensure that all external devices are protected by appropriate security software.

Ensure that access to all external devices is protected by appropriate security

equipment. cobas IT firewall must be used when the system is integrated into a

network.

Do not copy or install any software on the software control unit unless it is part of the

system software or you are nstructed to do so by a Roche Service representative.

It additional software is required, contact your Roche Service representative to ensure

validation of the software in question.

Do not use the USB ports to connect other storage devices unless you are instructed to

do so by official user documentation or a Roche Service representative.

Exercise utmost care when using external storage devices such as USB flash drives,

CDs, or DVDs. Do not use them on public or home computers while connecting to the

system.

Keep all external storage devices in a secure place and ensure that they can be

accessed by authorized persons only

Do not enter any confidential patient-relevant information into the work order file.

There is the risk of unauthorized access to patient data.

Notices

NOTICE List of notices

Before operating the system, read the notices contained in this summary carefully Failure

to observe them may result in damage to equipment.

Moving parts

Damage to the instrument due to contact with moving parts

Contact with moving parts may damage some components.

Keep all covers closed and in place while the instrument is operating.

Do not touch any parts of the instrument other than those specified. Keep away from

moving parts during instrument operation.

Hoche Diagnostics



Safety suniniary System Manual

Circuit breakers and fuses

Damage to the instrument or analyzer due to improper use

Should one of the instrument er analyzer circuit breakers or fuses blow, do not attempt tooperate the instrument or analyzer before contacting either your Roche Servicerepresentative or technical support.

Spillage

Malfunction due to spilled liquid

Any liquid spilled on the instrument or analyzer may result in malfunction, or damage ofthe instrument or analyzer.

Do not place samples, reagents, or any other liquid on the surface of the instrument oranalyzer other than in designated areas.

Do not place the microweli plate on any part of analyzer other than the microweli plateloader.

1f liquid does spul on the instrument or analyzer, wipe t up immediately and applydisinfectant. Be sure to wear protective equipment.

Roche Diagnostics



Systeni Manual

Safety labels on the system

Safety labels on the system

Warning labels draw your attention to areas of potential hazard. The labels and theirdefinitions are listed below according to their location.

The safety labels comply with the following standards: ANSI Z535.6, EN 15223-1,IEC 61010-1, or ISO 7000.

1f the labels are damaged, they must be replaced by Roche Service personnel. For

replacement labels, contact your local Roche representative.

Safety labels on the instrument

A Pipetting Arm

Do not move pipetting arm by hand.

B Biohazard warning

14r),, Instrument deck may contain biohazardous or chemicallycontaminated materials.

C Power connection

Connect only to earth-grounded outlet.

Connection to PC

Use only the appropriate shielded cables.

USB connection

Having a total cable distance of more than 5 m, signals can beinterfered.

Table 1-1 Description of safety labels on the instrument

Roche Diagnostics

Figure 1-1 Location of safety labels on the instrument

ID Label Meaning



Safety labels on the system Systeni .lv.tanual

ID Label Meaning

13 Barcode reader laser beam

Do not stare into beam of class 2 laser.

E Moving parts

Moving arm inside transparent cover. Aborts the run if cover isopened.

F Biohazard warning

,(ç).. Waste may contain biohazardous or chemically contaminatedmaterials.

Table 1-1 Description of safety labels on the instrument

Safety labels on the analyzer

Label Meaning Location

Consult the manual • On the analyzer type plate

Read the safety information contained inthis manual.

Hot surface • On the margin of the microweil

, Do not touch hot surfaces. plate loader• On the surface of the block cycler

cover• On the surface of the block cycler

unit• On the Xenon lamp unit,\ Biohazard warning • On the margin of the microweil

— Take adequate precautions when plate loader

working with potentially infectiousmaterial.

Table 1-2 Safety labels on analyzer

In addition to safety labels, there are safrty notes in the corresponding parts of thismanual and all other relevant manuals.

These safety notes give more detailed information about potentially hazardoussituations that may arise during daily operation or when carrying out maintenanceprocedures.

During operation, be sure to observe both the safety labels and the safety notes in allrelevant manuals.

Roche Diagnostics



Systern Manual Disposal

Disposal

Disposal of the instrument

lnfection by a potentially biohazardous instrument

The instrument must be treated as potentially biohazardous waste. Decontamination (ie., a

WARNING combination of processes inciuding cleaning and disinfection) is required before reuse,recycling, or disposal of the instrument.

1f you want to dispose of the instrument, contact your Roche representative.

Disposal of the analyzer

Infection by a potentially biohazardous analyzer

The analyzer must be treated as potentially biohazardous waste. Decontamination (ie., a

WARNING combination of processes inciuding cleaning and disinfection) is required before reuse,recycling, or disposal of the analyzer.

1f you want to dispose of the analyzer, contact your Roche representative.

Disposal of control unit components

Disposal of control unit components

Components of your control unit (such as the computer, monitor, keyboard) which are

marked with this symbol are covered by the European Directive on Waste E/ectr/ca/ andElectronic Equipment C,VEEE, 2002/96/EC).

These items must be disposed of via designated collection facilities.

For more information about disposal of your old product, please contact your city office,waste disposal service or your Roche representative.

Constraint: It is left to the responsible laboratory organization to determine whether controlunit components are contaminated or not. 1f contaminated, treat them in the same way as

the instrument and analyzer.

Roche Diagnostics



Disposal Systeni Mamal

Roche Diagnostics.


cobas® 4800 System 2 Overview

Table of contents Systeni Alanual

Overview

In this chapter you get a basic overview about the whole system inciuding theinstrument, the analyzer, and the software.

In this chapter Chapter

System overview 31

Instrument 32

Analyzer 33

System software and control unit 34

LIS 34

Consumables 35

Roche Diagnostics

System Maniial Version 1.0 29

2 Overview cobas® 4800 System


Roche Diagnostics

ao System Manual Version 1.0


Systern Manual Systern overview

System overview

The system provides a platform to perform qualitative and quantitative in vitronucleic acid amplification tests from biological specimens.

The system integrates fully automated total nucleic acid isolation directly fromprimary and secondary tubes, automated PCR setup, and real time PCR. The mainfeatures are:

• Fully integrated sample preparation

• Amplification and detection using real time PCR

• Minimal hands-on time

• Multiple sample types

• Multiple tests targets

• Intuitive operation by an easy to use workflow wizard

The system combines the following components:

LIS

Orders Results(test-specific) 4

—-

.

_ —

LK Control unit

Microweli plate

Samples with prepared samples

ReagentsConsumables

_____________________

Amplification and detectioncobas z 480 analyzer

Figure 2-1 System overview

Tests that only use the PCR Only workflow, have the following components:

cobas 4800 software

Result reports

S

Sample preparationcobas x 480 instrument

Roche Diagnostics


2 Overview

Systenz overview

cobas® 4800 System

System ivlanual

tControl ooit

LIS

t Resuits

•) .z=

cobas 4800 software

Result reports

Instrument

Roche Diagnostics

32

IVlicroweli platewith manually

prepared specimens

The instrument prepares the samples. The instrument is loaded with samples,consumables and reagents. After sample preparation, the microweli plate with thePCR-ready samples is unloaded, sealed, and transferred to the analyzer foramplification and detection using real time PCR.

The procedure for sample preparation is as follows;

1. Specimen-specific processing

2. Generic binding, washing, and elution

3. Working master mix preparation and PCR setup

0

Figure 2-2

Amplification and detectioncobas z 480 analyzer

System overview for tests which use only the PCR Only workflow.


cobas® 4800 System

Systeni Manual

2 Overview

Systeni overi’iew

Analyzer

Roche Diagnostics


The analyzer utilizes fluorescence signal to detect nucleic acids amplified by usingreal time PCR methodologv.

Sealing, loading, and unloading the microweli plate are the only manualinterventions.

33

2 Overview cohas® 4800 System

Systent overview

Figure 2-4

Systern Mannal

The system software runs on a dedicated control unit. The software guides the userthrough the entire process from sample preparation to amplification and detectionand result interpretation.

A hand-held barcode reader is connected to the control unit. It is used to scan reagentand reagent reservoir barcodes during loading of reagents as well as sample barcodesto set up the ivork order file.

For details about the control unit and the hand-held barcode reader, see Control unit

(p. 69)

The system can be connected to a Laboratory information system (LIS). Orders aredownloaded automatically from the LIS after samples are loaded onto theinstrument. After reviewing of the final results, results have to be manually uploadedto the LIS using the export function in the Results work area.

The System overview tab displays the status of the LIS connection.

Analyzer

System software and control unit

115

Roche Diagnostics



System Manual Systeni overvielv

os

[J [J .

A [IS disabled/not configured B LIS configured and transferring data

Figure 2-5 Example of LIS statuses

• Using result upload to LIS, results of the selected runs can be uploaded to the LIS. Theadministrator can define whether only accepted resuits or all results can be uploadedto the [IS.

• PCR Only runs are not fully supported by the [IS i.e. accepted results can be uploadedto LIS but work orders cannot be received from LIS. Use the sample editor to create thework orders for a PCR Only run.

• The LIS connection (if the LIS is present or not) can be configured by the lab manageror administrator.

• The LIS time-out (maximal time between an LIS query and answer) can be configuredby the lab manager or administrator.

For information about the LIS host protocols, refer to the cobas 4800 System HostInterface Manual.

Consumables

The system requires the following consumables:

• Pipetting tips

• Reagent reservoirs (200 mL and 50 mL)

• Deepweil plate

• Microweli plate and sealing film

• Small and large solid waste bags for tips

• Waste chute

• Waste container

For details about the consumables, see Consurnables (p. 58)

Roche Diagnostics


-*,—

A

Adby St4os

1 CTrSt4,

Aveb(y

L ISTrnsemn5

B

35

2 Overview cobas® 4800 System

Systern overview Systern Man,ial

Roche Diagnostics


cobas® 4800 System 3 Hardware

Table of contents Systevn Manual

Hardware

In this chapter you get an introduction into the instrument.

In this chapter Chapter F1Instrument 39

Covers 40

LEDs 41

Instrument deck 41

Autoload unit 43

Pipetting arm 45

1SWAP 46

Teaching needies 46

Waste station 47

Carriers 50

Sample carriers 50

Reagent carriers 53

Plate carrier 55

Tip rack carriers 55

Stationary carrier 56

Consumables 58

Pipetting tips 58

Reagent reservoirs 58

Deepweli plate 59

Microweli plate 60

Consumables for tip waste 61

Secondary tubes 61

Technical specifications of the instrument 61

Analyzer 65

Main building bio cks 65

LEDs 67

Technical specifications of the analyzer 67

Control unit 69

Hand-held barcode reader 69

Technical specification of the control unit 70

Roche Diagnostics


3 Hardware cobas® 4800 System

Table of contents Systens Manual

Roche Diagnostics

38 System Manual Version to


The instrument is an automated multi-channel pipetting instrument used to extract,purify, and prepare target nucleic acid for subsequent PCR testing on the analyzer.After sample preparation, the microweli plate with the PCR-ready samples isunloaded, sealed, and transferred to the analyzer for amplification and detectionusing real time PCR.

The procedure for sample preparation is as follows:

1. Specimen-specific processing

2. Generic binding, washing, and elution

3. Working master mix preparation and PCR-setup

Depending on the test, the instrument is able to process up to 96 samples (94 patientspecimens plus two controls) in a single run.

The main parts of the instrument are shown in Figure 3-1.

InstrumentSysteni Manual

Instrument

Roche Diagnostics


A Pipetting arm with pipetting head,8 pipetting channels, and ISWAP

B Instrument deck

C Autoloader with barcode reader

Figure 3—1 Instrument used for sample preparation

D Stationary carrier with heater/shaker unit,magnet plate, and holders for microweliplate and deepweli plate.

E Autoload tray

39

3 Hardware

Instrument

Covers

cobas® 4800 System

Systeni Manual

NOTICE

Roche Diagnostics

40

The following figure shows the covers of the instrument.

B Front cover

Figure 3-2 Covers of the instrument

The front cover protects you from moving parts inside the instrument. The frontcover can be opened for user intervention during maintenance. Always close thefront cover when you have finished maintenance work. During a run, the front covermust be closed.

Loss of materials due to forced opening of front cover

The front cover is locked during a run. While t is possible to force the front cover open

during a run, doing so will cause an emergency stop. The run will be aborted and all onboard reagents and in-process samples will be lost. Do not attempt to start the run withcover open.

A Left side cover C Right side cover



Systeni Manual

LEDs

Instrument

The loading status on the instrument deck is indicated by an LED bar above theautoload tray. The status LEDs inform you where to place the carriers on theautoload tray and which tracks on the instrument deck are occupied by a carrier.

A Track position

B [ED bar above the autoload indicating the loading status

Figure 3-3 [ED bar with status [EDs

LED status Meaning User action

No light No carrier loaded, No action necessary.

Green light steady Carrier on board at that No action necessary.position.

Green light blinking Indicates the track positions Place the carrier at thein which the carrier must be indicated positions on theloaded. autoload tray and insert the

carrier until the stop hooks.

Table 3-1 Status LEUs on LED bar

Instrument deck

The work area of the instrument is called instrument deck. The instrument deckhoids:

Roche Diagnostics


• removable carriers for samples, reagents, plates, and consumables.

• a stationary carrier used for sample processing. The stationary carrier is notremovable and hoids heater and shaker unit, magnet plate, and the plate holdersfor the deepweil plate and the microweil plate.

41


Instrument System Manual

The instrument deck is divided into 54 equal tracks. The tracks are numbered so thatyou can readily identify the location where a carrier must be loaded. The trackpositions are stamped on the surface of the autoload tray. A corresponding LED onthe LED bar above the autoload tray indicates the loading status of each track.

Track assignment is test-specific. The instrument deck layout below shows you anexample of the areas for each carrier type.

A Plate carrier for deepweli plate and microwell plate

B Tip carrier (left)

C Sample loading area

D Depending on the test, sample loading area or tip carrier (middle)

Figure 3—4 Example of the instrument deck layout

Track positions(test-specijic)

The following table summarizes the track positions on the instrument deck.

Track position Used for carrier

1-6 Platecarrier

7-10 Not used

11-16 Left tip carrier

17-34 Sample loading area (varies depending on the test)

29-34 Middie tip carrier

35-40 Right tip carrier

4 1-47 Stationary carrier for sample preparation

48-49 200 mL reagent reservoir carrier

50 50 mL reagent reservoir carrier

51-53 Reagent carrier

54 Not used

Table 3-2 Track positions on instrument deck of the instrument

Roche Diagnostics

42

Sample loading area The sample loading area can hold any combination of sample carriers.

For additional details about sample carriers, see Sample carriers (p. 50)

Instrument deck layout

E Tip carrier (right)

F Stationary carrier used for sample processing

G Reagent area for reagent reservoir carriers (200 mL and 50 mL)and reagent carrier



NOTICE

Roche Diagnostics


The autoload unit consists of the autoload tray - the platform where the carriers areplaced - and the autoloader. The autoloader detects waiting carriers with their tubesand containers and scans the barcodes.

The autoload unit is used to automatically bad carriers onto the instrument. Thecarriers are inserted by the operator into their designated position on the autoloadtray. The correct loading position is indicated by a blinking LED on the LED barabove the autoload tray.

jiJ For details about the status LEDs, see Table 3-1 Status LEDs on LED bar (p. 41)

After correct placement the carriers are loaded automatically onto the instrumentdeck by the autoloader. During loading, the barcode reader on the autoloader scansthe carrier barcode and the barcodes of the supplies on the carrier (samples, reagents,and disposables).

A Inserted carrierwaiting to be loaded

B Slide block

C Track position stamped on the autoload tray

Figure 3—5 Autoload unit with autoload tray and autoloader

The autoload tray contains slide bio cks that engage tracks in the carriers to guide thecarriers when they are loaded. When inserting a carrier onto the autoload tray, besure that the tracks on the carrier properly engage the slide blocks. Insert the carriersinto their designated position on the autoboad tray until they touch the stop hooks onthe far side of the tray.

Insert the carriers into the tracks between the front and rear slide blocks of theAutoboad tray until they touch the stop hooks on the far side of the tray.

Instrument damage due to improper carrier handling

Make sure the carriers are inserted completely until they touch the stop hooks on the

autoload tray Exercise care when inserting the carriers - do not push carriers against the

stop hooks with excessive force.

InstrumentSysteni Manual

Autoload unit

Inserting carriers on autoload tray

D Autoloaderwith barcode reader

E Autoload tray

43


Instrument Systeni Manual

Safety guards The autoload tray has safety guards attached on each side. Extend the safety guards toavoid bumping into the carriers on the autoload tray.

Personal injury due to bumping into carriers on autoload tray

Keep safety guards on both sides of the autoload tray extended to avoid bumping into

carriers on the autoload tray

Autoloader with barcode reader During loading, the barcode reader on the autoloader scans the barcode of the carrierand those of the supplies on the carrier (samples, reagents, and disposables).

The following barcode types are supported:

• Codabar (without check sum)

• Code 39 (without check sum)

• Code 128, subset B and C (with check sum)

• GTIN (inciuding JAN) (with check sum). This barcode type is not enabled bydefault. 1f you require this barcode type, contact Roche Service.

• Interleaved 2 of 5 (without check sum). This barcode type is not enabled bydefault. 1f you require this barcode type, contact Roche Service.

For details about barcode specifications, see Barcode reader (p. 63)

Auto matically unloading samplecarriers

Roche tiiagnostics

The instrument can automatically unload sample carriers i.e. samples, when pipettingis finished. This allows you to further process or store the samples without having towait for the run to finish. You can also define that the sample carriers be left in theinstrument and manually unloaded when the run is finished.

CAUTION

• S --

è --‘-

1

A Satetyguard

Figure 3—6 Satety guards on each side of the autoload tray



Systeni Manual

Pipetting arm

Instrument

The instrument is equipped with a pipetting arm containing eight pipetting channelsand the iSWAP device. During operation, the pipetting arm moves left-and-right (xdirection), picks up the required number of disposable pipetting tips, aspirates,dispenses, and mixes the liquids, and then ejects the used tips into the tip solid wastebag.

Each air-displacement pipetting channel can move forward-and-back (y-direction)and up-and-down (z-direction) during the pipetting operation. A disposablepipetting tip is picked up by each pipetting channel at the beginning of a pipettingcycle. The pipetting tip is ejected into the tip solid waste bag at the completion ofpipetting for that cycle.

Figure 3-7 Pipetting arm of instrument

Roche Diagnostics

Each pipetting channel contains a pipette stop disc which aligns the disposablepipetting tip when it is picked up by the pipetting channel at the beginning of apipetting cycle. Aspiration and dispensing is achieved by air displacement. Thepipette stop disc does not contact the liquid that is being aspirated into and dispensedfrom the disposable pipetting tip. The pipette stop discs must be cleaned on a weeklybasis.

For additional details, see Weekly niaintenance (p. 110)

A Pipetting channel C Pipetting arm

B Pipette stop disc



Instrument

iSWAP

Teaciting needies

System Manual

The landscape iSWAP is a robotic arm that picks up deepweli plates and microweliplates and moves them to the desired location on the instrument deck during a run.The ISWAP is mounted on the pipetting arm.

Figure 3-8 ISWAP

Roche Diagnostics

The instrument uses eight teaching needies to automatically check (and adjust ifnecessary) z-positioning and over- and under-pressure of each pipetting channel atthe appropriate time. The teaching needies are stored near the waste station, next tothe tip waste. The teaching needies are cleaned during the preventive maintenancevisit.

Figure 3-9 Teaching needles

A iSWAP

A Teaching needle



Systern Manual

Waste station

Safety information

Instrument

Roche Diagnostics


Make sure that you have read and understood the chapter General safety information(p. 13). The following safety messages in particular are relevant:

Warning messages:

Infection by biohazardous waste (p. 19)

Contanination of the environment by liquid waste and solid waste (p. 19)

Tip waste Solid vaste bags hold used pipetting tips after they have been ejected by the pipettingarm.

The instrument can be installed on either a bench top or on a trolley thataccommodates a larger solid waste bag.

• 1f the instrument is installed on a bench top, a small solid waste bag is used. Thissolid waste bag has a capacity for tips of at most one full run.

E9 Exchange the small solid waste bag each time before starting a new run to avoid overfillingof the tip waste.

For details about replacing the small solid waste bag, see Daily niaintenance (p. 105) andVeekly niaintenance (p. 110)

A Initialization/waste block

B Support frame

C Small solid waste bag with a capacity for tips of at most one full run

Figure 3—10 Small solid waste bag

47


Instrument

Roche Diagnostics

Systeni Manual

1f the instrument is installed on a special trolley, a plastic waste chute is used inplace of the solid waste bag and the tip waste is directed into a waste box on thetrolley that hoids a large solid waste bag. The large solid waste bag holds tips of atmost three full runs.

• The waste chute and waste box cannot be reused and must be replaced when they arefull.

• 1f required, replace the waste chute in the same way as the small tip solid waste bag.

• 1f required, fold up a new waste box as indicated in Figure 3-12 Folding up a new wastebox (p. 49)

For details about replacing the large solid waste bag, see Daily maintenance (p. 105) andWeekly maintenance (p. 110)

A Wastechute

B Large solid waste bag with a capacity of atmost three full runs

Figure 3-11 Waste box with large solid waste bag

Waste box The waste chute and waste box cannot be reused and must be replaced when they arefull. Fold up a new waste box in the following way:

C Waste box

D Trolley



Systern Manual Instrument

Liquid waste The liquid waste from the instrument is collected in an external waste container. Thelevel of the liquid waste is monitored by the system and a warning is issued when it isnot possible to do a full run. In this case, it is not possible to start the run.

The liquid vaste is emptied during daily or weekly maintenance. The liquid wastecontainer is reusable.

For details about emptying the liquid waste container, see Daily maintenance (p. 105) and

tVeekly maintenance (p. 110)

A

A Liquid waste cap with level detection sensor and waste tube

B Liquid waste container

Roche Diagnostics

Figure 3-13 Liquid waste container

Figure 3-12 Folding up a new waste box

//


3 Hardware

Instrument

Carriers

cobas® 4800 System

System Manual

A Insert the liquid waste cap as indicated B Close the liquid waste cap

Figure 3—14 Inserting and closing the liquid waste cap of the liquid waste container

The following carriers are used:

Camer for Carrier Used for

Sample carriers

Primary and secondary tubes.

For additional details, see Secondaytubes (p. 61)

Primary and secondary tubes.

For additional details, see Secondary

tubes (p. 61)

Collection medium primary tubes

200 mL reagent reservoirs

Roche Diagnostics

Different sample carriers allow the use of samples in primary and secondary tubes.

Depending on the test, up to 94 patient specimens can be loaded onto the instrument

per run.

The sample barcodes must face to the right of the carrier.

Samples 24-position sample carrier

32-position sample carrier

Collection medium carrier

Reagents 200 mL reagent reservoircarrier

50 mL reagent reservoir 50 mL reagent reservoirscarrier

Reagent carrier Reagent and control vials (in adapter)

Plates Plate carrier Deepweli plate and microweli plate

Tips Tip carrier Pipetting tip racks

Sample preparation Stationary carrier Heater/shaker unit, magnet plate, holdersfor plates

Table 3-3 Carriers used in the system



Systeni Manual Instrument

Each run has test specific controls e.g. positive/negative control. Controls are loadedtogether with the reagents onto the reagent carrier.

NOTICE Instrument damage due to the use of inappropriate or closed tubes

Using the incorrect tube types or closed tubes en sample carriers can damage theinstrument

Use only specified tube types for sample carriers.

Do not use closed tubes en sample carriers. Always open tubes on all sample carriers.

Barcode dirnensions c B c

U.

EL1

A

A Label length: max. 80 mm

B Code Ienght: max. 74 mm

C Quiet zone: min. 3 mm

D Label width: min. 12 mm

E Code width: min. 12 mm

F Distance from code to label edge: max. 1 mm

Fi9ure 3-15 Barcode dimensions

Positioning barcode labels on The barcode must fit within a range of between 20 mm and 100 mm from the bottomsample tubes of the tube.

100 mm

2OmmL

Figure 3—16 Fixing barcodes to sample tubes

Make sure the bars are perpendicular to the tube.

For additional details about barcode types and specifications, see Barcode reader (p. 63)

Positioning barcode labels oncontainers

Figure 3—17 Fixing barcodes to containers

Roche Diagnostics


3 Hardware

Instrument

cobas® 4800 System

Systenz Manual

24-position saniple carrier(test-specflc)

CAUTION

Container Range Note

PreservCyt 5 mm - 55 mm The barcode must fit within a range of between 5 mmand 55 mm from the bottom of the container

SurePalh’ 5 mm -40 mm The barcode must fit within a range of between 5 mmand 40 mm from the bottom of the container

Table 3-4 Positioning barcode labels on containers

The 24-position sample carrier hoids up to 24 primary or secondary tubes.

An aliquot can be manually transferred from the primary tube to the secondary ifnecessary.

The 24-position sample carrier uses one track on the instrument deck.

EJ3 For details about the types of tubes you can use on the sample carrier, refer to the testspecific package insert.

Infection by samples and associated materials

1-track carriers (such as a sample carrier) can fall over and cause injury or contamination.

Handle 1 -track carriers with particular care, position them on the autoload tray or placeseveral carriers together to minimize this risk.

Roche Diagnostics

A Carrier barcode8 Primary or secondary tubes

Figure 3-18 24-position sample carrier

The 32-position sample carrier is optionally available and hoids up to 32 primary orsecondary tubes.

An aliquot can be manually transferred from the primary tube to the secondary tubeif necessary.

The 32-position sample carrier uses one track on the instrument deck.

For details about the types of tubes you can use on the sample carrier, refer to the testspecific package insert.

The collection medium carrier is optionally available and hoids up to 12 Collectionmedium primary tubes.

This carrier uses two tracks on the instrument deck.

Open the collection medium containers before inserting the carrier on the autoload tray.

t—

•1v

,- S.

B

32-position sample carrier(test-specfic)

Collection medium carrier(test-specfic)


cobas® 4800 System

Systern Man ual

3 Hardware

Instrument

Reagent carriers

Reagent reservoir carriers

Roche Diagnostics


A Collectiori medium primary tube

B Carrier barcode

[igure 3—19 Example of a collection medium carrier

The reagent reservoir carriers hold the reagent reservoirs. The reagent reservoircarriers are available in two sizes:

• 200 mL reagent reservoir carrier for 200 mL reservoirs

• 50 mL reagent reservoir carrier for 50 mL reservoirs

The required reagents are poured into the reagent reservoirs which are then placedonto their dedicated positions on the reagent reservoir carriers. The reagent reservoirbarcodes must face to the right of the carrier.

For details about reagents and the placement on reagent reservoir carriers, refer to thetest-specific Operator’s Manual.

A 200 mL reagent reservoir

B Carrier barcode

Figure 3-20 200 mL reagent reservoir carrier

Aø

53


Instrument

A 50 mL reagent reservoir

B Carrier barcode

Systeni Manual

Figure 3—21 50 mL reagent reservoir carrier

Reagent carrier The reagent carrier hoids the test-specific reagents for sample processing and PCRsetup (controls, master mix, metal co-factor(s), and so on).

The required reagents are decapped and then placed onto their dedicated positionson the reagent carrier. The reagent barcodes must face to the right of the carrier.

For details about reagent placement on reagent carriers, refer to the test-specificOperator’s Manual.

The reagent carrier is the same carrier as the 24-position sample carrier.

NOTICE

Roche Diagnostics

Instrument damage due to the use of closed reagent vials

Using closed reagent vials on reagent carriers can damage the instrument.

Do not use closed reagent vials on reagent carriers. Always open reagent vials on

reagent carriers.

A Adapter with reagent vial

B Carrier barcode

Figure 3—22 Reagent carrier

g

A



Systent Manual

Plate carrier

Instrument

The plate carrier hoids the deepweli plate and the microweli plate. The deepweil plateis used to process the samples. The microweli plate is used to hold the final preparedsamples that are ready for PCR.

Place the deepweil plate on position 1 and the microweli plate on position 3 of theplate carrier. The other positions on the carrier are not used. The deepweli platebarcode must face to the right of the carrier. The deepweil plate barcode is readduring loading of the plate carrier. The microweil barcode is read after loading beingbrought in front of the barcode reader on the autoloader by the iSWAP.

At the end of the run, the plates are placed back on the plate carrier. Unload the platecarrier, seal the microweil plate and dispose of the deepweil plate according to thelocal regulations unless further off-the-system use is intended.

Tip rack carriers

Figure 3-23 Plate carrier

The tip rack carriers hold the tip racks with the disposable pipetting tips. Dependingon the test, up to three tip rack carriers can be loaded for a single run holding a totalof 15 tip racks.

The tip rack barcodes must face to the right of the carrier.

Roche Diagnostics

The total number of pipetting tips per run varies and depends on several criteria (test type,

sample media, run size, and so on)

The instrument tracks tip usage from run to run. The instrument checks if enough pipetting

tips have been loaded to perform the run. 1f there are not enough, a message is displayed.

To avoid this message, fully bad all the required tip rack carriers for each run.

Partially used racks can be used in next run.

To perform a run, all the required tip rack carriers must be loaded into the instrument.

A Deepweli plate on position 1

B Microweli plate on position 3



Instrument

Stationary carrier

Figure 3-24 Tip rack carrier

Systeni Manual

The stationary carrier is the area where the samples are processed. It is mounted onthe instrument deck and is not removable. The stationary carrier hoids four units:

• heater/shaker unit

• magnet plate

• deepweli plate holder

• microwell plate holder

A Microweli plate holder

B Deepweil plate holder

Figure 3-25 Stationary carrier

Heater/shaker unit The heater/shaker unit provides consistent and reliable heating and shaking duringsample processing.

A Tip raak with disposable pipetting tips. Each tip rack holds 96 tips.

C Magnet plate

13 Heater/shaker unit

Roche Diagnostics



Systern Manual Instrument

The heater/shaker unit is powered from an external controller box located outside ofthe instrument. The heater/shaker unit must be switched on and offon the externalcontroller box.

Do not forget to switch on the heater/shaker unit on its external controller box.

Always switch off the heater/shaker unit before unplugging It.

A

P Power switch of the heater/shaker unit

Figure 3-26 Controller box for heater/shaker unit

Magnetpiate The magnet plate immobilizes magnetic glass particles during sample processing.

Be aware, that the magnets are not affixed to the plate so any metal can remove the

magnets from its holder.

Figure 3-27 Magnet plate

Holdersfor deepweil plate and The holders for the deepweli plate and the microweli plate are where the washing andmicroweliplate PCR setup occurs during sample processing.

Roche Diagnostics

A Magnet on magnet plate

System Manual . Version 1.0 57,



Consumables

NOTICE Instrument damage and incorrect resuits due to use of unsuitable consumables

Use of non-Roche consumables may damage the instrument or lead to incorrect resuits.

Use only Roche consumables designed for use on the system.

Do not reuse consumables. All consumables are designed for one time use only.

Inspect consumables before use. Do not use damaged consumables.

Do not use consumables that have exceeded their expiry date. Replace expiredconsumables with unexpired consumables before sample processing.

Pipetting tips

Disposable pipetting tips with filters are used for pipetting of all liquids duringsample processing. The pipetting tips are available in tip racks of 96 tips each. Tipracks are placed into tip rack carriers.

For details about tip rack carriers, see Tip rack carriers (p. 55)

NOTICE Instrument damage due to use of unsuitable tips

Non-Roche tips may cause contamination or damage pipetting channels.

Use only disposable tips that are specified by Roche.

Figure 3—28 Tip rack with 96 disposable pipetting tips

Reagent reservoirs

The reagent reservoirs hold the reagents used for sample preparation. The reagentreservoirs are barcoded and are filled manually by the operator (scan-scan-pourplace principle) for each run.

Scan-scan-pour-placeprinciple To minimize handling errors the reagent reservoirs are filled and placed using thescan-scan-pour-place principle:

1. Scan the barcode of the required reagent using the hand-held barcode reader.

2. Scan the barcode of an unused reagent reservoir using the hand-held barcodereader.

3. Pour the reagent in the scanned reagent reservoir.

4. Place the filled reagent reservoir onto the required position of the reagentreservoir carrier as indicated in the wizard.

Roche Diagnostics



Systern ?vlanual Jos trument

Reagent reservoir sizes The reagent reservoirs are available in two sizes:

• 200 mL reagent reservoirs

• 50 mL reagent reservoirs

Reagent reservoirs are placed in reagent reservoir carriers.

For details about reagent reservoir carriers, see Reagent reservoir carriers (p. 53)

• The reagent reservoirs are designed for one time use. The software tracks the use of

the reservoirs and rejects previously used reagent reservoirs.

• Do not fiN reagent reservoirs above the maximal filI height. A sign within the reagent

reservoir indicates the maximal fili height.

• Always pour the entire reagent vial in the scanned reagent reservoir to avoid

underfilling.

• Handle filled reservoirs with particular care to avoid spiashes and tipping over.

• It is advisable to pour the reagent into the reservoir in a lengthwise movement to

minimize the risk of spiashing and resulting reagent loss.

• Do not pour reagents into reservoirs that are already placed onto a reagent rack.

Always follow the scan-scan-pour-place principle.

• Do not reuse reagents from previous runs.

A 200 mL reagent reservoir B 50 mL reagent reservoir.

Figure 3-29 Reagent reservoirs

Deepweli plate

The deepweil plate is used for sample processing. The deepweil plate hoids up to96 samples.

The deepweil plate is placed in the plate carrier on position 1 prior to a run.

For details about the plate carrier, see Plate carrier (p. 55)

• The deepweli plate is barcoded and designed for one time use. The software tracks the

use of the plate and rejects previously used deepweli plates.

• Open the primary packaging of the deepweli plate before use. Open the packaging

only in a clean environment to prevent contamination of the plate.

• Never touch the weNs of a deepweli plate to avoid contamination.

• Do not seal the deepwell plate before loading the plate into the instrument.

Roche Diagnostics


3 Hardware

Instrument

NOTICE

Microweli plate

cobas® 4800 System

Systeni !ulanual

The microweli plate (AD-plate 0.3 mL) hoids the processed samples mixed withworking master mix reagent and is used for amplification and detection on theanalyzer.

The microweli plate is placed in the plate carrier on position 3 prior to a run.

For details about the plate carrier, see Plate carrier (p. 55)

After final sample processing on the instrument the microweil plate is placed back onthe plate carrier by the iSWAP. Unload the plate carrier and seal the microweli plateusing the sealing film.

iJ For details about sealing of the microweli plate, refer to the test-specific Operator’sManual.

Roche Diagnostics

The microweil plate is barcoded and designed for one time use. The software tracksthe use of the plate and rejects previously used microweli plates.

• Open the primary packaging of the microweli plate before use. Open the packagingonly in a clean environment to prevent contamination of the piste.

• Never touch the weils of a microweil piste to avoid contamination.

• Do not seal the microweli piste before loading the piste into the instrument.

[

Figure 3-30 Deepweil piste

Instrument damage due to use of unsuitable deepweil plates

Use only deepweil plates designed for the instrument.


cobas® 4800 System

System A’fanual

N

3 Hardware

Instrument

Br

A Microweil plate

[igure 3-31 Microweli plate

B Sealing film

NOTICE

Consumables for tip waste

Instrument damage due to use of unsuitable microweil plates

Use only microwell plates designed for the instrument.

The following consumables are used for the tip vaste.

Small solid waste • Small solid waste bag for tips

Large solid waste • Large solid waste bag for tips

• Waste chute

• Waste box

Secondary tubes

The waste chute and waste box cannot be reused and must be replaced when they are full

For additional details, see Wiiste station (p. 47)

You can use specific tubes when a secondary tube is needed on the instrument for a24-position or 32-position sample carrier.

For details about the types of secondary tubes you can use, refer to the test-specificpackage insert.

The use of any tube other than those described, may lead to incorrect results orprocessing failures.

Technical specifications of the instrument

Roche Diagnostics


Every effort has been made to ensure that all the information contained in these

specifications is correct at the time of printing. However, Roche reserves the right to make

any changes necessary without notice as part of ongoing product development.

61



Table 3-5 Physical dimensions

Power requirernents

Systern principles

Environmental conditions

Item Technical details

Line voltage 115 VAC (-15%) to 230 VAC (+10%)

Line frequency 50 or 60 Hz (±5 Hz)

Power consumption Max. 600 VA

Installation category II

Fuses (delayed action) 115 V—: 6.3 A

230V—: 3.15A

Table 3-6 Power requirements

Item Technical detail

Principle The instrument is an automated multi-channel pipettinginstrument used to extract, purify, and prepare targetnucleic acid for subsequent real time PCR testing on theanalyzer.

Table 3—7 System principles


Temperature Running conditions: 15-30°C (59-86°F)

Transport and storage: -25 to ÷70°C (-13 to ÷158°F)

Humidity Running conditions: 15-85%, without condensation

Noise <65dBA

Pollution Level 2 (EN 61010-1, IEC 60664-1)

Altitude 30-2000 m (100-6500 ft) above sea level

Table 3—8 Environmental conditions

Roche Diagnosties

Saniples Item Technical detail

Sample type For test-specific sample types refer, to the test

specific package ïnsert.

On-board capacity Depending on the test, up to of 94 patient specimen canbe loaded per run.

Different sample carriers allow the use of samples inprimary and secondary tubes.

Table 3-9 Samples

Physical dirnension

Width

Depth

166.5 cm (65.55 in)

Height


Weight

101 cm (39.76 in) with loading deck

120 cm (47.2 in) with carriers on loading deck

90.5 cm (35.6 in)

Approximately 180 kg (397 ib)

Controls

Kit controls


Table 3-10 Controls

For test-specific kit controls, refer to the test

j specific package insert.



Systenz Manual

• Codabar (without check sum)• Code 39 (without check sum)• Code 128, subset B and C (with check sum)• GTIN (inciuding JAN) (with check sum)• Interleaved 2 of 5 (without check sum)

Instrument

Note: GTIN and Interleaved 2 of 5 barcode types are notenabled by default. 1f you require these barcode types,contact Roche Service.

Supported characters SP!#$%&O*. 1234567890:;<=>@ABCDEFGHIJKLM(Code 128 B and C) NOPQRTSUVWXYZ\ []A_’abcdefghijklmnopqrstuvw

xyz{}+

Note: \ A & should not be used in any manual entryfield (e.g. specimen barcodes, comments)

Not supporled characters /,Del(Code 128 B and C)

String length Maximum 20 characters, excluding start, stop andcheck characters. Depends on label length.

For Codabar and Interleaved 2 of 5, the minimum is 4characters, excluding start, stop, and check characters.

. For all other supported barcode types, the minimum is 2characters, excluding start, stop, and check characters.

Code density tolerance Best reading performance with X dimension between0.19 mm (0.0075 in) and 0.25 mm (0.01 in)

Quiet zone 10 times the X dimension, atleast 3 mm (0.12 in).

Print quality • Printing with ANSI / CEN / ISO grade A or B isrequired.

. Suitable for offset, typographic, intaglio andflexographic printing.

. Not suitable for mechanical dot-matrix and thermomatrix printing.

Table 3-11 Barcode reader

Interfaces Item Technical details

User interface Software running on the software control unit.

Instrument interface The instrument is connected to the software control unitthrough a USB connection.

Place the software control unit close to the instrument.Use the originally delivered USB cable only.

Table 3-12 Interfaces

Waste Item Technical details

Solid waste • Small solid waste bag holds used pipetting tips of atmost one full run.

. Large solid waste bag holds used pipetting tips of atmost three full runs.

Liquid waste Liquid waste container holds liquid waste.

Table 3-13 Waste

Roche Diagnostics

Barcode reader

Barcode types




Instrument Systeni Manual

Consumables Item Technical details

Transport temperature All consumables are designed to be transported withoutthe need for refrigeration at a temperature rangebetween -15°C to 55°C (5°F to 131°F).

Storage temperature Microweil plate and deepwell plate are designed to bestored at a temperature range between 15°C to 25°C(59°F to 77°F).

Pipetting tips can be stored al a temperature rangebetween -15°C to 55°C (5°F to 131°F)

Table 3-14 Consumables

Heater/sizaker unit

Roche Diagnostics

64


Line voltage 100-240 VAC

Line frequency 50-60 Hz

Power consumption 70 VA

Table 3-15 Heater/shaker unit



Systern Manual

Analyzer

Analyzer

The analyzer is a rapid thermal block cycler with integrated real-time detectioncapabilities.

Multiplex real time PCR assays allow the simultaneous detection of signals fromrnultiple dyes. This leaves It open how many filters are used by different IVD assays.As a benefit of this, multiple resuits can be reported from a single run.

NOTICE

Main building blocks

Thermal block cycler unit

Analyzer damage and incorrect resuits due to unsealed microweil plate

Before loading the microweli plate into the analyzer, it has to be sealed properly with the

self-adhesive sealing film. Sealing the plate is crucial to eliminate evaporation at high

temperatures. Unsealed microwell plates may damage the analyzer or lead to incorrect

results.

Always seal the microweil plate before loading the plate into the analyzer.

For details about sealing of the microwell plate, refer to the test-specific Operator’s

Manual.

Figure 3-32 Analyzer

The main building blocks of the analyzer are the following:

• Thermal block cycler with block cycler cover, ventilation, microwell plate loader,and microweil plate barcode reader.

Roche Diagnostics

Detection unit Consisting of the following:

• Lamp unit housing the Xenon excitation lamp

• Optics unit, including the liquid light guide, emission and detection filter wheel,and the CCD camera.



Analyzer Systern Manual

A Lamp unit

B Hausing

C Status LED

D Laad buttan

H Filter wheels

1 Black cycler daar (apen] with ventilation

H

BÇ

F Micrawell plate laader

G Detectian unit

E Thermal block cycler fans

Figure 3—33 Building blocks af the analyzer

Roche Diagnostics

66 System Manual . Versian 1.0


Systern Manual

LEDs

Analyzer

The front of the analyzer provides two status LEDs which inform the operator of thehardware status. The bad button for opening and closing the microweil plate loaderis bocated next to the two LEDs.

A Status LEDs

B Load button

Figure 3-34 Status LEDs and microweil plate loader

Technical specifications of the analyzer

Every effort has been made to ensure that all the information contained in these

specifications is correct at the time of printing. However, Roche reserves the right to make

any changes necessary without notice as part of ongoing product development.

Physical di,nensions

Power requirernents


Width 57.4 cm (22.6 in)

79cm (3 1.1 in) with extended plate loader

Depth 58.8 cm (23.1 in)

Height 49.7 cm (19.6 in)

Weight 55kg (121.25 ib)

Table 3—16 Physical dimensions


Line voltage 200-240 V/AC

Roche Diagnostics



1!.)

1

C Extended microweil plate loader

67


Analyzer Systern Manual


Line frequency 50 or 60 Hz

Power consumption 1500 VA

Fuses (delayed action) Primary fuses:

• 250V/TIOA

Secondary fuses:

• F1:250V/T3.15A• F2:250V/T8A• F3:250V/T16A

Lamp fuse:

• 250V/T2.5A


Safrty classflcations

Systern principles

Environmental conditions

Interfaces

Consurnables

Roche Diagnostics

68


Protection class T

Installation/overvoltage category II

Electromagnetic emission class B

Table 3—18 Safety classifications

Technical detail

The analyzer performs amplification and detection using real time PCR.

Table 3-19 System principles


Temperature Running conditions: 15-32°C (59-90°F)

Transport and storage: -25 to ÷60°C (-13 to ÷140°F)

Humidity Running conditions:

Max. 80% at 32°C, without condensation

Min. 30% at 15°C to 32°C

Noise <60 dBA

Altitude 0 to 2000 m (0 to 6500 ft) above sea level

Table 3—20 Environmental conditions


User interface Software running on the software control unit.

Instrument interface The analyzer is connected to the software control unitthrough an Ethernet LAN.

Table 3-21 Interfaces


Transport temperature The microweil plate is designed to be transported withoutthe need for refrigeration at a temperature range between-15°C to 55°C (5°F to 131°F).

Storage temperature The microweli plate is designed to be stored at atemperature range between 15°C to 25°C (59°F to 77°F).

Table 3-22 Consuma bles


cobas® 4800 System

System Manual

Control unit

3 Hardware

Control unit

A dedicated control unit runs the software, controls the instrument, and the analyzer.

CAUTION

Hand-held barcode reader

Incorrect resuits and malfunction due to use of unauthorized software

Use only manufacturers original installation CD-ROM or DVD sets for the operatingsystem, and the original software.

Any manipulation of system data files or other information determining or affectingsystem functions can result in erroneous results or equipment failure.

Only use the control unit that is supplied with the system.

Control unit with display gooseneck

A

A hand-held barcode reader is connected to the control unit. It is used to scan reagentand specimen barcodes during creation of the vork order file for microweli platepreparation.

Supported barcode types

Roche Diagnostics


The following barcode types are supported:

• Codabar

• Code 39

1A Display

B Display gooseneck

C Control unit

Figure 3-35

69

3 Hardware

Control unit

cobas® 4800 System

Systenz Manual

• Code 128, subset B and C

€iEjl For supported characters for the code 128 barcode type, see Barcode reader (p. 63)

• Data matrix (Roche-manufactured reagents only)

• GTIN (inciuding JAN) This barcode type is not enabled by default. 1f you requirethis barcode type, contact Roche Service.

• Interleaved 2 of 5. This barcode type is not enabled by default. 1f you require thisbarcode type, contact Roche Service.

Usage The barcode label is read by holding the head of the barcode reader in close proximityto the barcode label and then pressing the button on the barcode reader. The barcodeID is then automatically read and displayed on the screen.

Be sure to hold the head of the hand-held barcode reader over the correct barcode label.

It is recommended to visually verify the displayed scanned characters with the human

readable characters on the barcode label.

Figure 3-36 Hand-held barcode reader

Technical specification of the control unit

Software Operating system Windows 7

Database Oracle Database Enterprise Edition

Hand-held barcode reader Type 1T4600

Interface The hand-held barcode reader is connected to the control unitthrough the USB interface.

Skew angle ±40 degrees

Pitch angle ±40 degrees

Motion tolerance 10 cm (4 in) per second

Scan contrast 45% minimum for Matrix codes

3 7.5% minimum for all others

Temperature Operating: 0-50°C (32-122°F)

Storage: -40 to +70°C (-40 to +158°F)

Humidity 0-95% non-condensing

Roche Diagnostics


cobas® 4800 System 4 Software


Software

In this chapter the software basics are explained.

In this chapter Chapter LI

Basic software elements 73Colors 74

Tabs 74

Buttons 75

Lists 76Organizing lists 76Sort by column 77Column header context menu 77Displaying and hiding columns 77Filter drop-down list 78

Custom AutoFilter 78Managing filters and advanced filtering 79

Tool tips 79Wizard 80

Database 81Audit trail 81

Roche Diagnostics


4 Software cobas® 4800 System


Roche Diagnostics



System Manual

Basic software elements

Basic software elenzents

The screen of the software is divided into the following dedicated areas making thesoftware easy to understarid and intuitive to use:

Status area

• Tab navigation bar

• Main work area

• Global action bar

Alarm area

The screen representations shown in this chapter and throughout this manual are for

illustrative purposes only. The screens do not necessarily show valid data.

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A The status area displays the currently logged Din user as well as and date and time.

B The tab navigation bar displays the tabs.Choose a tab to open t. In the first row of thenavigation bar, the tabs of the main workareas are displayed. In the second row, thesubtabs belonging to the currently selectedwork area are displayed.

C This is the main work area. It displays thecontent of the currently selected tab.

Figure 4-1 Software screen

The global action bar contains buttons usedfor general software functions. Thesebuttons are always available.

E The alarm area displays the most recentalarms and warnings that are not yetconfirmed by the operator. Select an alarm inthe list and choose the Alarm button on theleft to get more details about the selectedalarm.

Roche Diagnostics

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Basic software elements Systenz Manual

Colors

The software uses the familiar traffic light color scheme.

Color Meaning

S Normal condition. The status is 0K.

Green

I Warning condition. Status is not 0K, but immediate intervention is

Yellow not required.

. Alarm condition. Immediate intervention is required. Operation

Red may have stopped.

S The item is selected or active.

Blue

Table 4-1 Color concept

Tabs

Tabs are used to group information and software functions into units that can bedisplayed on one screen. The second row of tabs represent subgroups of the tabselected in the first row. The tab in the third row is a subtab of the tab selected in thefirst row second row.

Navigating within the software needs only one or two clicks.

L Choose a main tab in the first tab row. Here you have access to the five main workareas Overview, Workpiace, Resuits, Messages, and Utilities.

2. Choose a subtab in the second row. Here you have access to all tabs of the selectedwork area.

The Workpiace tab is displayed only if a run is active.

A1’TPi..’ Resuits Messges Ul5ttes

B— ste,,

C—

A Main tabs. Overview is selected. The first row of tabs give access to the main work areas.

B Subtabs. System is selected. The second row of tabs show all tabs of the selected work area.

C Subtab belonging to lnstruments tab. It is only visible t the Instruments tab is selected.

Figure 4-2 Main tabs and subtabs

Roche Diagnostics



Systern Manual Basic software elerneuts

Buttons

Text buttons Choose a button to start the associated function. Some text buttons have a triangularmarking in a corner. This triangle telis you what exactly happens on screen if youchoose the button.

Button Behavior

r 1 Performs a specified action in the current windowCanceI j

A triangle in the top right corner of a button telis you that a newL J dialog box will be displayed when you choose the button.

r 1 A triangle in the bottom left corner of a button Leus you that theL J current window or dialog box will be closed when you choose the

button.

Table 4—2 Triangular markings in text buttons

Global action buttons On the right side of the screen, the global action buttons are available. They arealways visible and perform the following functions:

Button Name Use for...

. New run Starting a new run

[ ij A wizard will guide you through the whole run.

Abort Aborting a run

U The Abort Run dialog box is displayed when several runs

Abart are active. Select the run you want to abort.

ï 1Exit Exiting the software.

Exit

Editor Opening the sample editor

ilihi Opens the window for manually creating a new work

EJ order file. Orders are stored in an XML-based work orderfile. Work order files are used when the system is notconnected to an LIS or if the LIS is not working.

Export Exporting the audit trail and result counters.

‘€1Export

Table 4-3 Global action buttons

Roche Diagnostics



Basic software elements Systern Alanual

Button Name Use for...

Print Printing results, reports, messages, result counters, and

L_J alarms

A preview window is displayed allowing to configureprinting options.

Log on, Log off Logging on and off.

[)‘ The button label will change depending on whether the

Log user is logged in or logged off.

IEILog oS

Info Accessing the manuals and displaying the installedsoftware versions and licensing information.

Table 4-3 Global action buttons

Lists

The software provides powerful sorting and filtering tools for information displayedin tables. These allow a lengthy list to be condensed in ways that provide fast access toitems of interest. It is also possible to hide certain columns, display additionalcolumns, and change their left-to-right order.

This section just gives a general overview. Some functions are not available in some ofthe work areas, or less options are available, eg. in a context menu.

Organizing Iists

The sorting and filtering tools are accessed by right- or left-clicking the respectivecolumn headings.

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A Click the column header to sort the table in ascending or descending order. The sort order isindicated by an arrow.

B Right-click the column header to display context menu for sorting and grouping informationitems.

C Click the filter symbol (funnel icon) to display a list with appropriate filter options for thiscolumn.

Figure 4-3 Displaying the filter options

Roche Diagnostics



Systeni Pvlanual

Sort by column

Basic software elements

Click a column header to sort the table by the entries of this column. Successive clicksswitch between ascending and descending sort order, the order is indicated by thearrow that appears in the header.

Column header context menu

Not every column is sortable. 1f a column is sortable, en arrow indicating the sorting

direction will appear in the column header after clicking the column header.

Right-click any column header to display a context menu with further sorting andgrouping options.

A

C

0 — Rmove This Column

E — Column Chooser

—BestFit

Best Fit (all columns)G

A Select the sort order, or dear any sorting.

B Group listed items by the values of thiscolumn (dick + or - next to individualgroups to reveal or hide the items theycontain).

C Display a box with a graphic representationof the grouped items. Create nested groupsby dragging column headings to the displaybox above the list (dick + or - toexpand/collapse nested levels andshow/hide items within a level.

Remove the selected column from the table.

Add or remove a column from the table

Auto-adjust the selected column foroptimum display width.

G Auto-adjust all columns for optimum displaywidth.

Displaying and hiding columns

Figure 4-4 Column sort and group context menu

Roche Diagnostics

Right-click a column header and select Column Chooser.

Figure 4-5 Column Chooser dialog box

The Column Chooser dialog box contains all available information items that are notincluded in the table. Which items are available depends on the table from which youstarted the Column Chooser.

SortAscending

Sc’rt Descending

f’lear Scrtinq

Group Bylhis Column

Show Group By Box

D

E

F



Basic software elernents Systern Manual

To add a column (information item) to the table, select the item in the ColumnChooser and drag it to the appropriate place in the table header.

To remove a column from the table, select its header and drag it into the ColunmChooser.

Some columns (e.g Sample ID, Flags) are mandatory and cannot be removed.

Filter drop-down list

A filter symbol (funnel icon) is displayed in the column header of all columns thatcan be filtered. Right-click the filter symbol and a drop-down list appears.

c1

Date/time 1!)A 1(011) Adn

(Custoro) Âdn(Oonko)(Non btonlçs)12-Apr-2010 00:00:00

12-Apr-2010 00:00:00

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A Select Custom to display the Custom AutoFilter dialog box for reflning the filter criterion.

B Select the item that should serve as a filter criterion.

C Click the filter symbol (tunnel icon) to display the filter context menu.

Figure 4—6 Filter context menu

When a filter criterion is applied, its details are displayed in a bar at the bottom of thelist (A).

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Figure 4-7 Alter details bar

To return to the full view at any time (no filtering), choose the close button in thefilter details bar. Prevlously used filter settings remain accessible from the filterhistory.

For more information, see Managingfilters and advancedfiltering (p. 79).

Custom AutoFilter

The Custom AutoFilter option is available only in those columns that have a filtersymbol (funnel icon) in their column header.

With the help of the Custom AutoFilter you can apply one or two filter conditions,logically linked by AND or OR.

Click the filter icon in a column heading and select (Custom) to display the CustomAutoFilter dialog box.

Roche Diagnostics

78 System Manual - Version 1.0


Systern Manual Basic software elernents

Figure 4-8

Managing filters and advanced filtering

A Primary filter condition

B Secondary filter condition (optional)

C Box for typing a value

D Logical operator linking the two filter conditions

Custom AutoFilter

When a filter criterion is applied, its details are displayed in a bar at the bottom of thelist. This bar allows convenient selection of previously selected filter conditions (filterhistory) as well as disabling and enabling the criteria respectively.

Tool tips

AB C DE\ 1 II

A Click to close the filter details bar andremove all filters.

B Click to switch current filter on and off.

C Current filter condition

Figure 4-9 Filter control bar

For information about filtering in the Resuits work area, refer to the test-specificOperator’s Manual.

Tool tips provide brief functional descriptions when the mouse is paused over a toolor application button. They mainly occur in the sample editor and give informationto the user when there is a mistake in editing.

Test Information

Creation 2701.2011 15:53:50

Microweli Plate ID

Oarcode is mandator_L__B

A Box where an error occurred fl Tool tip informing about the nature of theerror

Roche Diagnostics


Figure 4—10 Example of a tool tip within the sample editor

[SeJentyj <Fatar

D Click to display previously used filters [filterlistory].

E Filter history list: Click a filter entry to applythis prevlously used filter.

79


Performing a system run requires the coordination of operator, instrument, andsoftware interactions. A wizard guides the operator through all processing steps andheips keep track of all necessary operator actions. The wizard is started by clicking theNew run button and ends with the display of the final PCR results. The run wizard isaccessible through the Workpiace tab.

A run goes through a series of steps. The next step can onlybe accessed if the currentstep has been successfully finished. Any step that has been finished is displayed as agreen box. The step that is currently in progress is displayed as a blue box. Any stepsthat have not been started are displayed as grey boxes.

For example, a PCR Only run may include the following steps:

I Lond

Figure 4—11 Steps in a run

It is not possible to go back to a previous step in a run. Follow the guidelines outlined in

this manual to avoid losing reagents, samples, or disposables.

A Run information

B Instructional area. Guides the operatorthrough all steps and gives feedback to theoperator.

Figure 4—12 Working with the wizard

D Button area for starting actions and abortingthe run.

Roche Diagnostics

Basic software elemeats

Wizard

Systeni Manual

End

24 LtARa,, 4447.444

— c

D

C Step time line


cobas® 4800 System

System Manual

Database

All data of the system are stored in an Oracle database.

4 Software

Database

Audit trail

Roche Diagnostics


The purge and archive function is used to archive resuits and purge them from thedatabase to free up space in the database for new resuits. Purge and archive should bedone much earlier before the database limit is reached.

Depending on the test, the amount of resuits that the database can store varies. Sometests store more information than others. The database has a storage capacity of up to100000 resuits.

No run can be started when the database has reached the maximal size. Use the purgeand archive function to clean up the database. To optimize performance, It isrecommended to purge and archive results older than 6 months.

For information about the purge and archive function, see Archiving (p. 90).

The purge and archive function only covers run data and results. Messages are kept in thesoftware until they are deleted manually. Therefore, it is recommended to manually deleteconfirmed messages from time to time to free up additional space in the database.

The actual size of the database is displayed in the System overview tab.

jr Li

‘—4,4—,—

‘-4,—

Figure 4-13 Database size in System overview tab

The software provides a secure, computer-generated, time-stamped audit trail torecord user activities that inciude the fo11owing

• Operator log on and log off

• Result acceptance, purging, and archiving

A

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81

4 Software

Database

cobas® 4800 System

Systeni Manual

• Configuration changes, inciuding changes in user accounts

• Interactions with LIS

• Audit trail changes (e.g. ifan audit trail was exported)

The audit trail of the software is designed based on guidelines in FDA Title 21 CFR,Part 11, Electronic Records: Electronic Signatures.

To access the audit trail, choose Messages > Audit trail.

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Roche Diagnostics

A List of user activities

B Information area

Figure 4-14 Audittrail

C Changes area

You can export the audit trail as a CSV file by selecting one or more entries andchoosing the Export button.

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Configuration

5 Configuration 85

cobas® 4800 System 5 Configuration

Table of contents Systern J’vianual

Configuration

In this chapter the configuration of the system and the export of support data isdescribed.

In this chapter Chapter II

Configuration 87

System settings 87

Reporting 88

Tests 89

Archiving 90

User management 92

Password management 92

Changing a password 92

User account management 93

Creating user accounts 93

Changing user accounts 95

Deleting user accounts 95

Unlocking user accounts 95

Rules 95

Account rules 96

Password rules 96

Exporting support data 97

Result counters 98

Roche fliagnostics


5 Configuration cobas® 4800 System

Table of contents Systeni Manual

Roche Diagnostics



Systern Manual Configuration

Configuration

The accessible configuration settings are dependent on the user group of the logged inoperator.

• Users assigned to the Supervisor group can access all configuration settingsdescribed below.

• Users assigned to the Operator group can only export support data (data for RocheService) and change their password.

The configuration tasks are divided into the following areas:

• System configuration

• User management

System settings

Utilities> Configuration> System settings

Use the System settings group to define the parameters found in Table 5-1 Systern

settingspararneters (p. 88).

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Figure 5-1 System settings group

Roche Diagnostics


S Configuration cobas® 4800 System

Configuration

Reporting

Systent Manual

Parameter Values Comment

Select the check box to ensure that the log ondialog box is displayed after starting thesoftware.

-, Utilities > Configuration > Reporting

The lab manager can use the Reporting group to specify the laboratory name andenable or disable the header of the result report.

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Figure 5-2 Reporting group

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0Det.ayt*Odfl,NIflflk9by

Roche Diagnostics

Enable automatic log on p- rdialog

Default vork order file folder Path name Location where the system looks for andsaves ivork order files. Type the full path anduse Windows naming conventions (e.g.C:\Temp\Workorders). Alternatively,

choose and browse for the path.

LIS connection was f7 F Select the check box to enable/disable LIS.configured

LIS timeout Number (2 to Maximum time between an LIS query and300) answer. The complete work order list has to

be completely transmitted within the settimeout, otherwise a timeout message willresult.

Maximum number of Number (1 to Maximum number of saved problem reportsproblem reports 1000)

Table 5-1 System settings parameters




Laboratory name Name The name of the laboratory that will be inciudedin the header of the reports.

Show Jaboratory header is p r Select the check box if you want the specifiedturned on header to be displayed on the reports.

Utilities> Configuration > Tests

Use the Tests group to disable or enable tests on the system. Disabled tests cannot berun on the system. You can also assign a test to a user group and sort the order of howthe test are displayed.

OtA,411(R) ?$eb-7flCI tUit ,I

U,.ID

Ove4viW •l R,its

3ttI*O

1 - -

Epot1 tippot d{ Rt S

Figure 5-3 Tests group


Test A workflow p r Select a check box to enable a test for use0fl the system. Clear the check box to

Test B workflow p F prevent a test from being used.

Sort order for workflow Number (0 to Define a number to sort the order of how‘Test A Full” 20) the test are displayed on the Select test

Sort order for workflow Number (0 to dialog box. For example, a number higher

“Test B Full” 20) than 0 will more the test downwards on theSelect test dialog box.

Workflow “Test A Full” is All From the drop-down list, choose a userallowed for group None group.

SupervisorOperator

Table 5-3 Tests parameters

Roche Diagnostics


Systern Manual

Tests

Configuration

Table 5-2 Reporting parameters

89


Configuration System Manual

Archiving

- Utilities> Configuration > Archiving

Use the Archiving group to define the settings for purging and archiving resuits.

The purge and archive function is used to archive resuits and purge themfrom theresuits database. This will free up space for new resuits in the database. Resuits arearchived at regular intervals in a password protected ZIP-file at a predefined location.Each run is archived in a separate ZIP-file.

• No manual intervention is necessary. The system performs purging and archiving ofresuits automatically based on the settings defined here.

• Ensure that the archive folder is inciuded in the backup plans.

• Contact Roche Service if result archives need to be viewed or restored.

• The purge and archive function only covers run data and resuits. Messages are kept inthe software until they are deleted manually Therefore, it is recommended to manuallydelete confirmed messages from time to time to free up additional space in thedatabase.

For information on how to delete confirmed messages, see Messages work area (p. 131).

,rrn41

Lh.,D

Overview Resuits Messages 10.103

___________________

Usurs Export support dsta Rosult 000310 a

54pR. su0..r03ro o0a f5Pifge 1.0 sOlo. 0300100.xsuOoamaedlofld ntiwh,0000

OWOx.e 000,loOei3xrxa,cOecuSr000ecflO.1 Mat,.n,,ç,Oreoss 110 RW000,zV OiOSrmr000efr,e0P.0,t,r0r0,YÇwrlOeot

Figure 5-4 Archiving group

Roche Diagnostics



System Manual CoJ/iguration


Maximum age of audit trail Number (10 to Number of days after which the audit

records 10000) trail records will be deleted.

Configured by the administrator.

Purge and archive p j’ Select the check box to enable thepurge and archive function.

Deselect the check box to disable thepurge & archive function.

Purge and archive path Directory path Location where the resuits arearchived. The archive folder can belocated on a server.

Type the full path to the archive folderand use Windows namingconventions. (e.g. D:\Archive)

Allernatively, choose and browsefor the path.

Maximum age of results Number (10 to 500) Number of days after which the resuitswill be archived and purged from thedatabase. All results that are older thanthe specified days will be archived andpurged.

To optimize performance, it isrecommended to purge and archiveresults older than 6 months(approximately 180 days).

Table 5-4 Archiving parameters

Roche Diagnostics



User management System lt’fanual

User management

Utilities> Users

There are three groups of functions available for managing users:

• Changing passwords

• Managing user accounts

• Setting up rules for passwords and user accounts

• Only users that are assigned as Supervisor can manage users and can set up rules for

passwords and user accounts.

• Users assigned as Operator can change their password only.

• Keep user access information on a secure place and do not make t public to prevent

unauthorized access to the system.

Password management

The initial password is defined during set up of a user account.

For more information, see Creating user accounts (p. 93).

Changing a password

Any user can change their password. Lab managers can change the passwords of allusers. The password must follow the password rules that are defined in the software.

For more information, see Password rules (p. 96).

To change the password

1 Choose Utilities > Users > Change password.

The Change password dialog box is displayed.

2 In the Old password box, type the current password.

3 In the New password box, type the new password.

4 In the Repeat new password box, type the new password again.

5 Choose the 0K button.

To change the password of another user

1 Choose Utilities > Users.

2 Select a user in the list.

3 Choose the Reset password button.

4 In the Password box, type the new password.

5 In the Repeat password box, type the new password again.

6 Choose the Apply button.

Roche Diagnostics


cobas® 4800 System 5 Cunfiguration

System ivlanual User management

User account management

The following functions are available:

• Creating new user accounts

• Changing and deleting existing user accounts

• Unlocking user accounts

Res W.esses - -

Epot ,ppohd,CU5 t VT1UWkce* UW - UW -

KI=’

-Ii

____

UW

_____

--

- -j

UWWW LJ

H)

1 -

•fl..aaflU,

Figure 5-5 Users area

User riglits A user assigned to the Operator group has the following user rights:

• Starting and aborting runs

• Viewing result details and accepting, exporting, and printing results

• Performing maintenance

• Confirming messages

A user assigned to the Supervisor group has the same user rights as the Operator

group plus:

• Editing configuration settings

• Managing user accounts and editing account rules

• Deleting messages

Creating user accounts

User name and password must be unique.

Roche Diagnostics


5 Configuration

User management

cobas® 4800 System

Systeni Manual

To define a new user account

1 Choose Utilities> Users> Create.

!._._.Figure 5—6 Defining a new user account

2 Type the User ID.

The user ID must be unique on the system.

3 Type the User name.

4 Select the user language.

5 Type the password and confirm it.

The password must follow the password rules that are defined on the system.

6 Assign the User groups.

To each group, a set of user rights is assigned.

7 Select the Enable automaticlog off check box to make sure that the user will beautomatically logged off after a certain period of inactivity on the system.

For more information, see Account rules (p. 96).

8 Select the Change password on next log on check box to ensure that the userchanges his or her password during the next log on.

9 Clear the Account is active check box if you are preparing a new user account tobe ready for a later date.

10 Clear the Password never expires check box if the user should change thepassword periodically.

For more information, see Account rules (p. 96).


This button is only active if all necessary definitions have been made.

Over ew Rcsuhs MessagesEpppoddst

Sza —,

t R___.,._

. rirr— ,,,,,..,,M.wop,,a S

r)

Roche Diagnostics



System Manual User management

Changing user accounts

To change a user account


2 Select a user from the list.

3 Choose the Edit button.

4 Make the necessary changes.


0Deleting user accounts

To delete a user account


2 Select a user from the list.

3 Choose the Delete button.

A confirmation dialog box is displayed.

4 Choose the Yes button to confirm the action.

0

Unlocking user accounts

By default, user accounts become locked after five unsuccessful logon attempts.Locked users are indicated in the Users list.

To unlock a locked user account


2 Select the locked user from the list.

3 Choose the Unlock button.

0

Rules

- Utilities > Users > Rules.

There are two sets of rules, one for user accounts and one for passwords.

Enter zero to switch 0ff a rule.

Roche Diagnostics



Accoont rules

Passnord eepny peciod (n days)

Attornahc Ing elf petiod (Nl rtin)

User bas bef n tocked die to nwahd Icg en

Figure 5-7 User account mies

1 so9

r—T 5

Item Values Comment

Automatic Log Number (0 to 999) Select or type the number of minutes ofoffperiod (in inactivity on the system after which the user ismin) automatically logged off.

User has been Number (0 to 999) Select or type the number of failed logonlocked due to attempts before the system automatically locksinvalid log on the account.

Table 5-5 User account settings

Password rutes

vald password roest have

mirumum roimber of characters

minrmum nunter of appercase characters TrntnfiTtlJll nurober & Inwercase r 1

mh,rn,uçnnundeeofdets rmlrsmum number of nondphanurrrenc characters (eg $5. %)

Figure 5-8 Password ruies settings

Item Values Comment

minimum number of Number Select or type the minimum number ofeharacters characters a password must consist of. The

minimal required value is automatically set bythe system based on the values of the otherpassword rules.

minimum number of Number Select or type the minimum number ofuppercase characters uppercase characters a password must contain.

minimum number of Number Select or type the minimum number oflowercase characters lowercase characters a password must contain.

minimum number of Number Select or type the minimum number of digits adigits password must contain.

minimum number of Number Select or type the minimum number of nonnonaiphanumeric alphanumeric characters a password mustcharacters (e.g. !, $, #, %) contain.

System Manual

Password expiry Number (0 to 999)period (in days)

Select or type the number of days after which theuser must change the password.

User management

Account rules

Password rules

Roche Diagnostics

Table 5—6 Password mies settings

96 System Manuai . Version 1.0


Systern Manual Exporting support data

Exporting support data

1f necessary, support data for individual runs or a batch of runs can be exported to an

external storage device. The support data will help Roche Service to support youoptimally.

114 5H—

- overvlew Resuits Mesnges

Veem w.,uIt counters

21-IETS 2012 145 T” A 23.l, 201214 IS St

231104-20,2 1420 0*1,4 02-110.2022142012 L44,emQ,, [E]

Figure 59 Export data for Roche Service

To export support data

1 Choose Utilities> Export support data.

2 Select the runs that were affected by the problem.

3 Choose the Extract support data button.

A dialog box for entering the folder for storage is displayed.

4 In the dialog box, select the folder where you want the exported data to be saved.

5 Follow the instructions of Roche Service how to send the data to them.

0

Roche Diagnostics



Result counters System Manual

Result counters

View information about the number of tests that were completed, failed, and invalid.

— Utilities > Result counters

C44a, 4SW Ct-2OI3j2 IU

U44U

Overyw Rs4!ts Messae I5NU,. —

Ur Epo4ppoid4t4 ;ÇWT! kW..F4.# F,,m T., -

441.448 ‘t 44 28 tÇ4

Figure 5—10 Viewing the resultcounters

To filter the result counter, activate the date filter, define a date range, and choose theUpdate counters button.

You can use the Export button to export the resuits counters as an XML file. Only thedisplayed resuits are exported.

You can use the Print button to print out the result counters.

Roche Diagnostics


Maintenance

6 Maintenance 101

cohas® 4800 System 6 Maintenance

Toble of contents Systern Monual

Maintenance

In this chapter the required maintenance procedures are described.

In this chapter .

Safety information 103

Instrument maintenance 104

Perform start up procedures 105

General cleaning for the instrument 105

Dailymaintenance 105

Weekly maintenance 110

Analyzer maintenance 115

General cleaning for the analyzer 115

Exchanging the Xenon lamp 116

Exchanging the ventilation dust filters 119

Exchanging fuses 122

Roche Diagnostics


6 Maintenance cobas® 4800 System


Roche Diagnostics


cobas® 4800 System 6 Maintenance

Systeni Manual Safety information

Safety information

Considerations before operation

Make sure that you have read and understood the chapter General safety information

(p. 13). The following safety messages in particular are relevant:

Warning messages:

• Electrical shock by electronic equipment (p. 18)

• Loss of sight due to staring into laser beam (p. 18)

• Infection and injuîy due to sharp objects (p. 19)

• Infection by samples and associated materials (p. 19)

• Infection by biohazardous waste (p. 19)

• Contamination of the environment by liquid waste and solid waste (p. 19)

• Explosion through sparks (p. 20)

• fire risk through usage of sprays (p. 20)

Caution messages:

• Personal injuîy due to contact with moving parts (p. 20)

• Skin infiammation or injury caused by reagents (p. 21)

• Personal injury due to hot surface (p. 22)

Safety precautions:

• Operator qualification (p. 16)

Observe the system safety labels illustrated and described on Safety labels on the

system (p. 25)

Before performing any maintenance, read the safety messages carefully. 1f you ignoresafety messages, you may suffer serious or fatal injury.

Roche Diagnostics



Instrument maintenance System Manual

Instrument maintenance

Maintenance for the instrument is initiated and managed directly from the software.The System tab shows the actual maintenance status of the instrument. Maintenanceis started from the cobas x 480 tab.

Periodic maintenance must be performed in order to ensure safe and reliableoperation of the instrument. A maintenance procedure is completed once theprocedure has been fully executed and the resuits are within the specifications.

Aborting maintenance procedures A maintenance procedure must always be finalized. Do not abort a maintenanceprocedure. Aborting a maintenance procedure will lead to a failed status, andmaintenance will need to be started again. After aborting a maintenance procedure,switch off the instrument and switch it on again after 10 seconds.


Always wear disposable gloves during maintenance. Pay special attention to the sharp

WARNING edges on the ISWAP and the pipetting channels.

Explosion through sparks

The liquids used for cleaning are flammable.

WARNING Do not clean the instrument in the vicinity of open flames or devices which could

create sparks. Do not use hot air blowers to dry the instrument.

NOTICE Instrument damage and malfunction due to incorrect maintenance

Perform only the maintenance actions described in the daily and weekly maintenance

procedures. No other maintenance is allowed on any module of the instrument.

The following maintenance intervals have to be followed:

Daily maintenance Recommended daily after instrument startup.

Weekly maintenance Recommended at the end of the week before shutting down the instrument.

1f an error is encountered during a maintenance procedure, try to resolve theproblem and re-start the maintenance procedure. 1f you cannot resolve the erroryourself, cail Roche Service.

Preventive inaintenance As part of the preventive service program two scheduled preventive rnaintenanceservice visits per year will be required. Preventive maintenance is performed byRoche Service. The duration of each preventative maintenance procedure will beapproximately 4 hours.

NOTICE Instrument damage and malfunction due to incorrect maintenance

Performing daily and weekly maintenance is mandatory. A run can only be started when

maintenance is complete.

1f any parts of the instrument or carriers have become contaminated, the weekly

maintenance procedure must be performed.

Do not shut down the control unit or the software during a running mainteriance

procedure.

Roche Diagnostics



Systeni Ivlanual Instrument maintenance

• Counters are reset to twenty-four hours when daily maintenance is performed. 1fweekly maintenance is performed, daily maintenance is not required on that day.

There is no processing icon like an hourglass or progress bar displayed duringmaintenance.

Perform start up procedures

The system control unit is normally left on, except for a daily restart (e.g. as part orbefore starting the daily maintenance).

It is strongly recommended to restart the system daily.

For startup procedures, if the control unit is powered off, refer to the test-specificOperator’s Manual.

General cleaning for the instrument

Safety

Make sure that you have read and understood the chapter General safety information(p. 13) and Safety information (p. 103)

The surface of the instrument should be cleaned on a weekly basis with a lint-freecloth moistened with deionized water. 1f a spul of reagents occurs, the instrumentshould be cleaned with a 70% ethanol solution.

Removable internal parts of the instrument, such as all carriers, should be weeklyrinsed with deionized water followed by 70% ethanol.The area around the instrumentshould be periodically checked to ensure that air flow around the instrument isunrestricted and that books, papers, or other supplies do not interfere with air flow.Ifa specimen or other biohazardous material spills on the instrument or any of theinstrument carriers, the area or carriers should be cleaned with a decontaminatingand nucleic acid destroying agent, followed by deionized water.

• Do not use other organic solvents (eg., petroleum, benzene, or other solvents) becausethey can damage plastic materials.

• Do not use an alcohol solution with a concentration greater than 70°/s because thismay damage transparent viewing windows.

• Only use completely dry carriers on the instrument.

Daily maintenance

The following tasks are part of the daily maintenance:

1. Shutdown and restart the system control unit.

2. Check 1f instrument deck is clean.

3. Empty the tip waste and the liquid waste container and clean the tip eject plate.

4. The instrument automatically checks the tightness of the pipetting channels.

5. The instrument automatically verifies the functioning of the liquid level detection.

Roche Diagnostics



Instrument maintenance System Manual

Tools and material required • Tip waste bag

• Disposable latex gloves

• Protective glasses

• Lab coat

To perform daily maintenance

1 Shutdown and restart the system control unit.

2 Log onto the software.

3 Choose Overview> System > cobas° x 480 tab.

4 Choose the Perform daily maintenance button.

The instrument initializes. The pipetting arm and the autoloader move to the lefthand side. A message box displays the first daily maintenance procedure thatmust be performed.

DaiIymatnIenore cIekdeckcteanog

Opoo tbofr toow 5 5kf th kned tob &and,

It de d,kode c4ts ootoe.

II U d ndoto be ded toeooCeeI Wttbedavmtenooe.Ineteed, peeonedMhdne o.eebty n,Ônnoe.

ILZ...i:z_:.JI 1

The operator now has access to the instrument deck to check if cleaning isrequired.

5 Open the front cover and inspect that all the parts of the instrument or carriersare clean.

• 1f the instrument deck is clean continue with step 6.

• 1f the instrument deck requires cleaning, stop daily maintenance. Performweekly maintenance. To stop daily maintenance, choose the Cancel button inthe message box.


The next message box is displayed.

Oaily rndiIItendnce tip wdste

the 14e wasoe ond peeso O+ to cordnoe.

Cel oel aboet the day raatetenanoe

j Cancel

7 Replace the tip waste bag as described below.

For additional details about the tip waste, see I’Vaste station (p. 47)


The tip waste, the tip eject plate, and the plastic waste chute must always be

CAUTION considered as biohazardous.

Replacing small waste bag

1f a small ivaste bag is used access the tip waste bag by lifting the instrument frontcover. Remove a full waste bag from the instrument by removing the supportframe from the initialization/waste block.

Roche Diagnostics



Systern Manual Instrument maintenance

Roche Diagnostics

A Initialization/waste block

B Waste bag or waste chute

Figure 6-1 Removing waste bag or waste chute

7When replacing the small waste bag, place the bottom portion of the waste baginside the support frame, fold the top over the frame and then place the supportframe into the initialization/waste block. Dispose of either waste bag and contentsaccording to the appropriate local regulations.

Replacing large waste bag

1f a waste container is used remove the large waste bag from the waste containerand replace it with a new one. Close the large waste bag with a binder and disposeof either waste bag and contents according to the appropriate local regulations.

• The waste chute and waste box need to be replaced when full and cannot bereused.

• 1f required, replace the waste chute in the same way as the small tip waste bag.

• 1f required, fold up a new waste container as indicated in Figure 3-12 Folding up anew waste box (p. 49)

C Tip eject plate

D Support frame


6 Maintenance cohas® 4800 System

Instrttnient nzaintenance Systern Manual

Roche Diagnostics

A Waste container with large waste hag

Figure 6-2

8 Remove the tip eject plate of the tip waste station (see Figure 6-1 Reinovingwaste

bag or waste chute (p. 107)) and clean it with disinfectant solution.

Put the clean tip eject plate back in place properly. Make sure the tip eject platefits horizontally on the initialization/waste block. 1f it is not placed back properly,this may cause a run to crash with instrument malfunction.

A

A Tip eject plate fits horizontally on the initialization/waste block

Figure 6-3 Replacing the tip eject plate properly

9 Check the status of the liquid waste container. Empty the waste container ifitrequires emptying. Dispose of the liquid waste according to the appropriate localregulations.

For additional details, see Liquid waste (p. 49)

Waste container

108 System Manual Version 10


Systeni Manuni

A Open the liquid waste cap.

Figure 6-4

Instrument maintenance


The procedure continues with the tightness check of the pipetting channels. Thepipetting arm will move to the right hand side to pick up the teaching needies.

Two checks are done with the pipetting channels, the over-pressure and theunder-pressure check.

flt TWI3 ITIB29 I7I&Z %171&ï4

Roche Diagnostics

For the capacitive liquid level detection check the needies are picked-up again.One channel to the next is checked for the proper functioning of the liquid leveldetection.

1f the automatic tightness or liquid level detection checks fail, repeat twice, then calI

Roche Service.

11 The pipetting arm and the autoloader move to the right hand side and the end ofthe daily maintenance wizard is displayed.

4) by

L-z:zz]I


The daily maintenance process status is saved.

0

B Lift the liquid waste cap carefully

Removing the liquid waste cap



1nstrumeHt ninintenance Systern Manual

Weekly maintenance

1f weekly maintenance is being performed, daily maintenance is not required on that day.

The following tasks are part of the weekly maintenance:

1. Shutdown and restart the system control unit.

2. Clean the instrument deck and the carriers.

3. Empty the tip waste and the liquid waste container and clean the tip eject plate,

the covers and the autoload protecting ribbon.

4. The instrument automatically checks the tightness of the pipetting channels.

5. The instrument automatically verifies the functioning of the liquid level detection.

Tools and inaterial required • Tip waste bag

• Disposable latex gloves

• Protective glasses

• Lab coat

• Paper towels

• Lint-free cloths or Q-tips

• Ethanol (70%)

• De-ionized water

• Decontamination liquid

NOTICE Infection by biohazardous materials

Use proper decontamination liquid according to the advice of Roche Service.

To perform weekly maintenance

1 Shutdown and restart the system control unit.

2 Log on to the software.

3 Choose Overview> System> cobas x 480 tab.

4 Choose the Perform weekly maintenance button.

The instrument initializes and a message box is displayed.

Weeky maItennte ctrnek uto(od tray-

Md. the,,,,, ,he , the

Cre ed b,.t the .e,,

Icz.:zz4

5 Remove all carriers from the autoload tray and then choose the 0K button.

The instrument deck is unloaded automatically. The procedure continues with

the tightness check of the pipetting channels. The pipetting arm moves to the

right hand side to pick up the teaching needles.

Two checks are done with the pipetting channels, the over-pressure and the

under-pressure check.

r_

Roche Diagnostics



Systenz Mannal Instrument maintenance

For the capacitive liquid level detection check the needies are picked-up again.One channel to the next is checked for the proper functioning of the liquid leveldetection.

1f the automatic tightness or liquid level detection checks fail, repeat twice, then caliRoche Service.

A message box displays.

Wcofdymofntenance - deckcloartlng

• Opeftfooo&ontherkok

(SooOpooot Monodto o of deoorto*otg d doo*&çfhdo,)

6 Clean all carriers with decontamination liquid and leave them to dry.

7 Open the front cover and wipe the instrument deck with a cloth saturated withdecontamination liquid. The slide blocks - the guides on the autoload tray forproper insertion of the carriers - in particular must be checked for cleanliness.


The pipetting arm and the autoloader move to the left hand side of the instrumentdeck and the next message box is displayed.

WeekLymafntennc . Upwaste

C’pso tto Frt oovo, on,ptyo,,ddoovthe t woot4) on poovs co to

(Sos Opooto,s Mov,off .o of oI’o’ns.ooisot Ond dsoordovdndingtlof.)

l[z2Z4

9 Replace the tip waste bag as described below.

For additional details about the tip waste, see Waste station (p. 47)


The tip waste, the tip eject plate, and the plastic waste chute must always be

CAUTION considered as biohazardous.

Replacing small waste bag

1f a small waste bag is used access the tip waste bag by lifting the instrument frontcover. Remove a full waste bag from the instrument by removing the supportframe from the initialization/waste block.

Roche Diagnostics



Instrument mainlenance Systeni Manual

Removing waste bag or waste chute

When replacing the small waste bag, place the bottom portion of the waste baginside the support frame, fold the top over the frame and then place the supportframe into the initialization/waste block. Dispose of either vaste bag and contentsaccording to the appropriate local regulations.

Replacing large waste bag

1f a waste container is used remove the large ivaste bag from the waste containerand replace it with a new one. Close the large waste bag with a binder and disposeof either waste bag and contents according to the appropriate local regulations.

• Waste chute and waste container can be reused and need to be replaced only ifrequired.

• 1f required, replace the waste chute in the same way as the small tip waste bag.

• 1f required, fold up a new waste container as indicated in Figure 3-12 Fo/ding up anew waste box (p. 49)

C D

A Initialization/waste block C Tip eject plate

B Waste bag or waste chute D Support frame

Figure 6-5

Roche Diagnostics


cobas® 4800 System

Systern Manual

Roche Diagnostics


6 Maintenance

Instrument niaintenance

A Waste container with large waste bag

Figure 6-6 Waste container

10 Remove the tip eject plate of the tip waste station (see Figure 6-5 Removing wastebag or waste chute (p. 112)) and clean 11 with disinfectant solution.

Put the clean tip eject plate back in place properly. Make sure the tip eject platefits horizontally on the initialization/waste block. 1f it is not placed back properly,this may cause a run to crash with instrument malfunction.

A Tip eject plate fits horizontally on the initialization/waste block

Figure 6—7 Replacing the tip eject plate properly

113


Instrument maintenance Systern Manual

NÖTJCE

Roche Diagnostics

11 Check the laser scanner window of the barcode reader on the autoloader andclean it with a lint-free cloth or Q-tips lightly soaked in ethanol (70%) to preventunreliable barcode scanning.

Malfunction due to soiled laser scanner window

The laser scanner window must be complet&y dry and free from dust and fibers before

the instrument can be reused.

12 Clean the front and side cover with a lint-free cloth soaked in disinfectantsolution and wipe dry.

13 Clean the autoload protecting ribbon with a lint-free cloth soaked in disinfectantsolution and wipe without exerting pressure.

14 Check the status of the liquid waste container. Empty the waste container if it

requires emptying. Dispose of the liquid vaste according to the appropriate localregulations.

For additional details, see Liquid waste (p. 49)

A Open the liquid waste cap.

Figure 6-8


The pipetting arm and the autoloader move to the right hand side and the end ofthe weekly maintenance wizard is displayed.

WeeI,ly ,nintenfle -

Wdy n,*ne efdy o.etd

rzJJ


The weekly maintenance process status is saved.

B Lift the liquid waste cap carefully

Removing the liquid waste cap



Systeni Manual Analyzer maintenance

Analyzer maintenance

No user maintenance is required for the analyzer. General cleaning of the analyzerand exchanging the Xenon lamp, the ventilation dust filters, and the fuses aredescribed below.


Never clean the analyzer without turning the analyzer power switch off and

WARNING disconnecting the power cable.

Do not pour fluids into the interior of the analyzer or onto any parts of the analyzer.


As with all potentially biohazardous specimens, universal safety precautions should be

WARNING taken when handling and processing samples. Spills should be immediately disinfected

with an appropriate disinfectant solution to avoid spreading contamination to

laboratory personnel or equipment. Handling and disposal of infectious material should

be performed according to local safety guidelines.

General clean ing for the analyzer

Regular cleaning of the analyzer and the accessories is not required. 1f necessary,clean the housing of the analyzer, the thermal block cycler, and the block cycler coverwith 70% ethanol.

Erroneous resuits due to dirty ventilation inlets

1f the ventilation inlets are not replaced regularly, the lense could get dirfy, and this could

WARNING cause an erroneous result.

Ensure that the ventilation dust filters are replaced twice a year.

Ventilation inlets The ventilation inlets of the analyzer should be checked regularly, to ensure anunrestricted air flow. You should ensure that the ventilation dust filters are replaced

twice a year.

For details, see Exchanging the ventilation dust filters (p. 119).

Roche Diagnostics



Analyzer nsaintenance Systern Ivlanual

Exchanging the Xenon lamp

The analyzer automatically and continually measures the intensity of the Xenon lampto ensure optimal detection of the fluorescent signals during real time PCR. 1f thelamp intensity falis below the minimum required intensity, a warning is issued by thesoftware that the Xenon lamp must be exchanged. The Xenon lamp is available as aspare part from Roche. Please contact your local Roche representative for details.

Safety information

Only use the Xenon lamp available directly from Roche.

WARNING Never exchange the Xenon lamp without turning the analyzer power switch off anddisconnecting the power cable. Non-compliance poses the danger of electric shockand damage to the eyes by the bright light of the lamp.

Before exchanging the Xenon lamp, make sure you have waited an appropriate periodof time (approximately 20 minutes) after you shut down the analyzer to allow the lampto cool. Directly after completion of a run, the lamp is hot enough to cause animmediate burn.

In its cold state the lamp has a high internal pressure. During operation, the internalpressure is higher than in the cold state. The lamp is extremely unlikely to explode butthe possibility cannot be entirely ruled out. Therefore, when handling the Xenon lampalways use the safety cover supplied. When installing the lamp, remove the safety coverand always take the following precautions: wear goggles and gloves and protect yourneck. Take the same precautions when removing the lamp.

Do not get finger marks, grease, paint, or similar materials on the bulb. Before usingthe lamp, remove any such marks with isopropanol, ethanol, or any other suitableagent that leaves no residues on the bulb.

The Xenon lamp does not contain any polluting material. The used lamp should bestored in its safety cover before disposal. Where possible, the lamp should be disposedof by a specialist waste management company. 1f this is not possible, put on protectiveclothing, wrap the lamp completely in leather or thick cloth, smash the lamp, includingthe discharge tube, with a suitable implement and dispose of the pieces.

To exchange the Xenon lamp

Roche Diagnostics

116

1 Remove the right panel of the analyzer as shown below.


cobas® 4800 System

Systern Manual

6 Maintenance

Analyzer nrnintenance

2 Move the cover of the analyzer to the right to access to the lamp unit.

------.<-

Roche Diagnostics


4. 1

3 Unscrew the lamp unit cover and open it.

1 cobas z 480

117

6 Maintenance


cobas® 4800 System

Systeni ManHal

4 The Xenon lamp is fixed by a clip which is secured by a screw. Unscrew the clipand open it.

.1

Roche Diagnostics

-/Ik.

,0% -

cbas z 480

A Safety clip B Xenon lamp

Figure 6-9 Xenon lamp with clip

5 Press the safety clip to lift the Xenon lamp out of its clamp and remove the twoconductors.

cobas z 480

Figure 6—10 Press the safety clips



Systeni Manual

A Conductor(-)

Analyzer nzaintenance

1B Conductor (+)

Figure 6-11 Remove the conductors

6 Instail the new Xenon lamp. First attach the (-) conductor and then the (+)conductor.

7 Complete the installation by following the above mentioned steps 4 to 1 exactly inthe reverse order.

• Make sure the (-) conductor points upward while fixing the new Xenon lamp intothe clamp.

• After replacing the Xenon lamp, reset the lamp counter by choosing the Reset

values after lamp exchange button in the software. The analyzer monitors theactual lamp intensity and lifetime. 1f either of the two expires, you will be informedand prompted to exchange the lamp. No run can be performed unless the lamp hasbeen replaced.

0

Exchanging the ventilation dust filters

NOTICE

Roche Diagnostics

The electronic rack of the analyzer is cooled by ventilation. Two ventilation inlets arelocated in the lower right corner of the right side of the analyzer (right beside theblock cycler compartment) and in the back of the analyzer. To avoid anycontamination of the analyzer’s interior by dust particles, these ventilation inletscarry dust filters.

Instrument damage due to insufficient maintenance

The dust filters should be exchanged once a year. There is no indication from thesoftware. You can order exchange dust filters directly from Roche.

-.\‘

:!!“ L._oosbas z 480


6 Maintenance


cohas® 4800 System

Systern Manuat

To exchange the ventilation dust filters

1 Remove the right instrument panel as shown below to access the lateralventilation inlet.

Roche Diagnostics

2 Remove the ventilation dust filter carrier.



Systern Manual Analyzer maintenance

3 In the same way, remove the dust filter carrier from the rear ventilation inlet.

Roche Diagnostics

Figure 6—13 Rearventilation dust filter

4 Remove the used dust filters from each carrier and insert new filters.

A Dust filter

Figure 6-14 Dust filters

5 Replace each dust filter carrier on the corresponding ventilation inlet andreassemble the analyzer’s panel by following the above mentioned steps 3 to 1

exactly in the reverse order.

0


6 Maintenance


Exchanging fuses

cobas® 4800 System

System Manual

The analyzer contains eight fuse types. Fuses must be exchanged when they areblown.

A High-breaking capacity (T 1OA H / 250V)

Figure 6-15 Primary fuses on the power box

Labeling Amperage/Voltage Consumer bad

FUSES LINE INPUT 2 x T 1OA H / 250V Line input analyzer

2 x T 1OA H / 250V

Table 6-1 Primary fuses

To access secondary fuses El — F5, remove the right panel of the analyzec

Roche Diagnostics


Always turn off the analyzer, then unplug the main cable before replacing fuses.

WARNING

Prirnaryfuses

Secondaryfuses

A High- or low-breaking capacity

Figure 6—16 Right side of power box, interior of the analyzer


cohas® 4800 System

Systeni Manual

6 Maintenance

Analyzer niaintenance

Labeling Amperage/Voltage Consumer bad

F1 T 3.15A / 250V Detection unit

F2 T 8A / 250V Black cycler unit

F3, F4, F5 T 16A / 250V Thermal block cycler Peltierelements

Table 6-2 Secondary fuses

A Right side of Xenon lamp module, above the lamp’s mains socket

Figure 6-17 Xenon lamp fuse

To access the Xenon lamp fuse, remove the cover of the analyzer.

AmperagelVoltage Consumer bad

2 x T 2.5A / 250V

Table 6-3

Xenon lamp

Roche Diagnostics


To exchange a primary or secondary fuse

1 Turn off the analyzer, then unplug the main cable.

2 Unscrew the cover of the fuse compartment by using a screwdriver.

3 Remove the cover together with the fuse from the chamber.

4 Exchange the blown fuse with a replacement fuse and place it back in thechamber.

5 Screw tight the cover again.

0To exchange the Xenon lamp fuse

1 Turn off the analyzer, then unplug the main cable.

2 Remove the cover of the analyzer.

3 The Xenon lamp fuse is located above the mains socket of the Xenon lampmodule.

Xenon lanipfuse

Xenon lamp fuse

123


Analyzer niaintenance Systern Manual

4 Using forceps, press the clamps of the left and right side of the fuse holder inward.PuIl the fuse holder out of its chamber.

5 Exchange the blown fuse with a replacement fuse and place the fuse holder backin the chamber.

6 Re-attach the instrument cover.

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Troubleshooting

7 Troubleshooting 127

cobas® 4800 System 7 Troubleshooting

Table of contents Systeni Manual

Troubleshooting

In this chapter alarm and troubleshooting information help to deal with exceptional

situations.

In this chapter Chapter.N

Overview 129

Messages work area 131

Reviewing and confirming new alarms 132

About result flags 134

General troubleshooting 136

Problem reports 136

Remote support 136

LIS troubleshooting 137

Hardware troubleshooting 138

Instrument 138

Barcode reading errors 138

Instrument connection problems 139

Run recovery 140

Remote support 140

Unloading the instrument deck manually 140

Take out of operation 141

Analyzer 141

Analyzer connection problems 141

Analyzer not working 141

Red status LEDs 142

142

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System Manual . Version 1.0 . 127

7 Troubleshooting cobas® 4800 System


Roche Diagnostics

128 System Manual •Version 1.0


System Manual Overview

Overview

The system records all problems originating from the software, instrument andanalyzer. The error records can be viewed in the alarm area at the bottom of thescreen and in the Alarms and Messages vork areas.

UwU1sbm,M

-

Overyrew Resuits Y.l4ttri-p UbirtiesAiarms ,,-,—;.r* Audrt Iran

Ø2!4.R, 4MUL: ..

A .

A Iiie alarm area displays the most recent alarms and warnings that are not yet confirmed by the

operator. Select an alarm in the list and dick the Alarm button on the left to get more details

about the selected alarm.

Figure 7-1 Alarm area

Alarm area The color of the alarm button changes depending on the severity of the alarms listedin the alarm area.

loon Purpose

1Red icon: the alarm area contains at least one error.

Yellow icon: the alarm area only contains warnings but no errors.

Table 7-1 Alarm button

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Oi’ervieiv Systeni Mawal

Message and alarm icons The severity of the alarms and messages is indicated by the following icons:

Icon Purpose

Designates an error message (red icon). The error must be resolved beforeadditional samples can be run. A problem report is generated automatically.

Ï?iiJ For details about problem reports, see Problen, reports (p. 136).

Designates a warning (yellow icon) indicating an error was detected but thesystem cao still be run.

Designates an informational message.

Table 7—2 Message and alarm icons

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cobas® 4800 System

Systeni Man ual

Messages work area

There are three tabs in the Messages work area.

7 Troubleshooting

Messages ivork area

Tab Description

Alarms Contains all alarms from the analyzer or the software that havenot yet been confirmed by the operator.

Messages Contains all information, error, and warning messages.

Audit trail Shows recorded user activities, e.g. operator log on and log off.

For more information on the audit trail, see Audit (rai!

(p. 81).

Table 7-3 Tabs in Messages work area

The purge and archive function only covers run data and resuits. Messages are kept in the

software until they are deleted manually. Therefore, it is recommended to manually delete

confirmed messages from time to time to free up additional space in the database.

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024,06w

A I’’”S nornioon 24 41002012160153 5262026

*e**rA 4100 23000-2612145514 6252421

Resuits 2,-0vfl.fl

Mossago; Audit tra,I

5p4146404 1100S446S4L42042MFIF40d4644fl4IWW4445244

p4,24,gon,nsa,a4a0Èa.tt.w4624u16446uz8gnn46u

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B —

D

E:IA All unconfirmed alarms are listed in the Alarms tab.

B Alarm details. Select an alarm in the list to see the alarm details.

C Choose the Report button to manually generate a problem report.

D Choose the Confirm button to confirm the selected alarm. Confirmed alarms are deleted fromthe Alarms tab, but are still listed in the Messages tab.

Figure 7-2 Alarms tab

131

7 Troubleshooting

Ivlessages ivork area

cobas® 4800 System

System Iianual

U5eD J),:

Overv:ew ResisAdit til

T.

A Use the sort, filter, and group functions in the column headers to customize the list ofmessages.

B Choose the Confirm button to confirm the selected message.

Figure 7-3 Messages tab

Field Description

Severity Contains an icon to indicate whether the message is an error,warning, or information message.

Date/time Displays the date and time when the message was generated.

Code Displays the message code.

Text Displays an abbreviated description of the error or situation thatoccurred.

Confirmation Displays date and time of confirmation.date/time

Confirmed by Displays the operator who confirmed the message.

Table 7-4 Fields in Messages tab

All alarms should be confirmed.

The selected alarm(s) are removed from the Alarms tab, but are stil listed in theMessages tab.

Choose . (Print) to print the contents of the Alarms or Messages tab.

Reviewing and confirming new alarms

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cobas® 4800 System 7 Troublesliooting

Systern Manual Messages work area

To confirm a new alarm

1 Choose Messages > Alarms or double-dick the alarm in the alarm area at the

bottom of the screen.

2 Select the alarm to be confirmed.

• To select several nonadjacent alarms, use the Ctrl key.

• To select a range of adjacent alarms, use the Shift key.

3 Choose the Confirm button.

0

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About resuitfiags Systeni Manual

About result flags

Flags are automatically generated with resuits ifduring processing certain technicalchecks were not passed, the result exceeds or does not reach predefined limits, or iftechnical or mechanical problems occurred during a run.

Results that do not have flags associated with them can be considered valid. However,not all results that have flags associated with them are invalid. Some flags arewarnings rather than error messages and do not necessarily invalidate the result(s).

Some flags are for information purposes only.

The flags may originate from either the analyzer, the software, or the resultinterpretation.

Result icons In the Resuits work area, icons help you identify if a result failed, is invalid, or has aflag.

Icon Comment

Result is invalid with one or more flags or failed.

Result has a flag.

(blank) Result is valid or has no flags

Table 7-5 Result icons

To help you easily identify a positive result, some tests highlight positive results.

To display result flag information

1 Choose the Resuits tab.

2 Select a result that has a flag entry in the Flags column.

Roche Diagnostics



Systern Manual About resuitfiags

3 Choose the Details button.

The details area is displayed. All flags that were generated for this result aredisplayed.

E F

/ Mesogs uti:t.j

____

_s_

___________

1 r-fr

A

_______________________________________________________________________

IIU .

B-’

/ \

_

/ \C D

A Selected result E Result icons

B Tab for displaying Flags F Flags column

C Flag code G Details area

D Flag description

Figure 7—4 Example of how to display flag information

Each flag is identified by its flag code, and information on the nature of the reasonfor each flag is displayed.

For a list of result flags, refer to the test-specific Operator’s Manual.

Roche Diagnostics



General troubleshooting Systern Manual

General troubleshooting

In this section, you find information about troubleshooting aids such as problem

reports and remote access.

Problem reports

A problem report is created by the system after every run, or when a new error

message is generated. 1f necessary, a problem report can also be created manually.

Problem reports are used by Roche Service to assist in troubleshooting cases.

Problem reports are stored as ZIP-files in a predefined folder where they can be

retrieved and sent to Roche Service when required.

lrhen the maximum number of problem reports is reached and another problem

report is added, the oldest problem report will automatically be deleted from the

folder. The maximum number of problem reports is defined under Utilities

> Configuration> System settings.

To retrieve a problem report

1 Open Win dows File Explorer and go to“C:\ProgramData\Roche\c48OO\ProblemReport’

2 Copy the requested problem report to a portable storage device.

3 Send the problem report to Roche Service together with a detailed problem

description.

0To manually create a problem report

1 In the software, choose Messages > Alarms.

2 Choose the Report button.

3 Retrieve the problem report as described above.

0

Remote support

In a remote support session, the software is remotely operated by Roche Service. Call

Roche Service to initiate a remote support session.

NOTICE Instrument damage diie to improper handling

Do not operate the software during a remote support session.

To initiate a remote support session

1 Request a remote support session at Roche Service.

Roche Service initiates a remote session. A message is displayed on screen askirig

to allow remote access on this computer.

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136 System Menual . Version 1.0


Systern Manual General troubleshooting

2 Confirm the displayed message.

The remote support session starts. The session is terminated by Roche Service.

0

LIS troubleshooting

1f you use LIS and are having problems, this will help you understand LIS statuses.

1f the connection to the LIS does not work, contact the local IT support to find out ifthere is a problem with the LIS. When the problem has been solved, disable andenable the LIS under Utilities > Configuration> System settings.

The System overview tab displays the status of the LIS connection.

Screen Status Comment

Not available LIS has been disabled underAb,tyS4s Utilities> Configuration>

LI ts System settings.

Transferring Data is being transferred to/fromthe LIS.

Trarewr5j

Not ready There is no connection to the LIS.For example, the network

LIS Trn,St, connection is down.55e

4Idie The connection to the LIS is

dreay.

Connecting Attempting to make a connectione to the EIS.Ceec5rç

Table 7—6 [IS statuses and meanings

lfJ For information about the LIS host protocols, refer to the cobas 4800 System Host

Interface Manual.

1f the LIS connection does not work and a run must be processed, you can disable LIS and

use the sample editor to manually create the work orders.

Roche Diagnostics



1f one or more barcode labels could not be read, an error or warning message isdisplayed. For example:

A Error message (example) C Manually enter or scan the barcode

B Barcodes that could not be read

Figure 7-5 Barcode error message

The reason for this error may be poor-quality, damaged, or missing barcode labels.There are several options for handling barcode errors.

E! Exactly follow the procedures outlined below to resolve barcode reading errors. Deviating

from this procedure might abort the run.

Systent Manual

A

Tube barcodes could not be reed Please reload carrier

Hardware troubleshooting

Hardware troubleshooting

Instrument

Barcode reading errors

Roche Diagnostics

Track Position Baicode

51 15

51 16

51 17

51 18

51 23

51 2411

138 System Manual Version 10


Systern Manual Hardware troubleshooting

To resolve barcode errors for reagents

1 Do one of the following:

1f the reagents have not been loaded into the instrument, select andmanually enter or scan the barcode with the barcode reader:

MmI B.d. Entry l1n.t8d £tV

Barod 56406019700901 Barcode

Reqype Barcode Retype Barcode 56406019700901

- 0K1

Figure 7-6 Manual Barcode Entry

1f the reagents have been loaded into the instrument, choose the Unloadbutton and wait until the carrier is unloaded. Choose and manually enteror scan the barcode with the barcode reader. To bad the reagents back intothe instrument, choose the Reload button.

( To resolve barcode errors for samples

1 Do one of the following:

• Choose the Unload carriers button and wait until the carrier is unloaded.Choose the Reload button. The carrier is unloaded and loaded again withoutany further user intervention. This time the carrier is loaded slower tofacilitate barcode reading.

• Choose the Unload carriers button. Under the Barcode ID field, manuallyenter the barcode. Choose the Reload button.

0Instrument connection problems

1f the connection between the software and the instrument is broken or if the instrumentwas switched off the run status may not be displayed correctly until the connection hasbeen re-established.

1f the connection between the control unit and the instrument is interrupted (i.e. theUSB connector is disconnected), the instrument will immediately abort the run. Thestatus of the instrument changes to Error, however the status of the run in thesoftware will only be updated after the connection is re-established. The same is truefor the display of the associated error message in the alarm area. An error messagewill only be issued after the connection to the instrument is re-established.

After a connection error the instrument has to be unloaded manually.

For details, see Unloading the instrument deck nianually (p. 140)

Roche Diagnostics



Hardware troubleshooting System Manual

Run recovery

1f the run control is lost by the software an automatic run recovery process is started.Depending at what time point in a run the run control was lost the recovery processcontinues the run or aborts it. Run control can be lost for reasons like power drops,shutdown of the control unit, or connection or hardware problems.

Results of such runs are flagged with flag M6 (analyzer) or MiO (instrument). Theflag only indicates that run recovery was initiated but does not indicate if the runcould be recovered by the system or not. To decide if the result is reportable analyzethe result itself and all associated flags as you would do with any result.

Remote support

In a remote support session, the software is remotely operated by Roche Service. CallRoche Service to initiate a remote support session.

Do not operate the software during a remote support session.

To initiate a remote support session

1 Request a remote support session at Roche Service.

Roche Service initiates a remote session. A message is displayed on screen askingto allow remote access on this computer.

2 Confirm the displayed message.

The remote support session starts. The session is terminated by Roche Service.

0Unloading the instrument deck manually

All carriers have to be manually unloaded from the instrument deck ifa run wasaborted and the carriers are not automatically unloaded.

Safety information

Take adequate precautions if the instrument deck has to be unloaded manually. Theinstrument deck or the carriers could be contaminated.

Make sure that you have read and understood the chapter General safety information(p. 13). The following safety messages in particular are relevant:

Warning messages:

• Infection by samples and associated materials (p. 19)

• Infection and injury due to sharp objects (p. 19)

Caution messages:

• Skin inflammation orinjuly caused by reagents (p. 21)

To manually unload the instrument after an instrument abort

1 In the wizard, choose the Unload button.

2 1f carriers are not unloaded automatically switch off the instrument.

Roche Diagnostics



Systeni Manual Hardware troubleshooting

3 Clear all obstructions and remove carefully all carriers from the instrument deck.

Be careful not to break the stop hooks. Unloading carriers manually causes stophooks to break easily.

Call Roche Service ifthere are any obstructions that can not be cleared.

4 Clean the instrument deck.

5 Switch on the instrument.

Check before switching on the instrument that no obstructions are left on theinstrument deck.

6 Perform daily maintenance.

Do not manually remove tips from the pipetting channels. Cail Roche Service ifthere are stili tips on the pipetting channels after daily maintenance.

For details, see Daily maintenance (p. 105)

0Take out of operation

Perform the following take out of operation procedure if the system is not used for alonger period of time.

1 Perform weekly maintenance of the instrument.

For details, see Weekly maintenance(p. 110)

2 Switch off the instrument and unplug the power cord and the USB cable from theinstrument.

3 Switch off the heater / shaker unit and unplug the power cord from the heater /shaker unit.

4 Log off the software, switch off the control unit, and unplug the power cord fromthe control unit.

0

Analyzer

Analyzer connection problems

1f the connection between the control unit and the analyzer is interrupted, the runwill continue and a warning is displayed. After re-connection the software willrefresh the status of the run.

The displayed maintenance status of the analyzer may not be correct. To get thecorrect maintenance status, refresh the analyzer under Overview> System > cobasz480 tab.

Analyzer not working

For error messages and flags, refer to the test-specific Operator’s Manual.

Roche Diagnostics



Hardware troubleshooting Systeni Manual

1f the analyzer does not function

1 Make sure that the analyzer is correctly connected to the power supply.

2 Check if the voltage on the analyzer’s type plate corresponds to the local voltage.

3 1f the analyzer stili does not function, contact Roche Service.

0Red status LEDs

1f the left and right status LEDs glow red

1 Restart the analyzer.

2 1f the LEDs stil! glow red, contact Roche Service.

For error messages and flags, refer to the test-specific Operator’s Manual.

Roche Diagnostics

142 System Manual . Verson 1.0

Glossary

cobas® 4800 System

Systern Manual

Glossary

Arnp4fïcation - Saniple carrier

The glossary explains key terms used in thisdocumentation.

Amplification The process of producing many DNAcopies from one original DNA or RNA target region.PCR is a nucleic acid amplification technique.

Anneal The biochemical process of hybridizing orbinding two segments of complementary nucleic acid.

Autoloader The hardware assembly on the instrumentthat enables automatic loading of carriers placed on theloading deck. It consists of a loading head movable in theY direction, which draws the items into the instrumentand can read the barcodes on them.

Control unit A personal computer that runs theMicrosoft Windows operating system and the software.

Controls Reagent formulated to produce known resuitsthat are processed like samples. The software monitorscontrol resuits. Each run requires a positive and anegative control.

Ct value The amplification/detection cycle where thegrowth curve crosses a specific fluorescence level and thegrowth rate can be observed.

Deepweli plate Plate used for extraction on theinstrument.

Denaturation The process of separating doublestranded DNA into single strands by breaking thehydrogen bonds.

Detection Obtaining measurements to determinewhether a sample is reactive for the target analyte.Fluorescence measurements are made at selectedtemperatures and times during the amplification process.When the run is complete data are analyzed to determinethe presence of the amplified products from the targetand internal control nucleic acid sequences.

DNA Deoxyribonucleic Acid (DNA) is the geneticmaterial that is passed from parent to progeny andpropagates the characteristics of the species in the formof genes it contains and the proteins for which it codes.DNA contains the following four nucleotides: dATP,dCTP, dTTP, and dGTP.

Instrument deck The work surface of the instrument,where pipetting takes place. It is organized as a left-toright series of tracks, into which the autoloader drawscarriers.

LAN Local Area Network. The system control unit iscon nected to the instrument and the analyzer.

Roche Diagnostics

115 Laboratnry information system. A computerizedsystem for entering, managing and reporting laboratoryinformation. Information includes but is not limited topatient demographics, test orders, and test results.

Loading deck The external shelfat the front of theinstrument. It provides a surface onto which carriers canbe placed before the autoloader draws them into theinstrument.

Magnetic glass particles Used in combination withother reagents to bind nucleic acids, allowing separationof impurities during washing.

MGP see Magnetic Glass Particles.

Microweil plate Plate used for amplification anddetection. The 96-well plate is barcoded and has to besealed with a special sealing film before inserting into theanalyzer.

PCR Polymerase Chain Reaction. The in vitro processused to amplify short specific target nucleic acidsequences. PCR is performed by cycling the temperatureof the amplification mixture according to a set profile.The profile generally consists of denaturation andannealing.

Pipetting channel A hardware assembly mounted onthe pipetting arm. It can pick up and eject tips, aspirateand dispense liquid, and detect liquid level in tubes.There are 8 pipetting channels working in parallel.

Pipetting tip A disposable tip for pipetting. The tipsused by the instrument are capable of transferring up to1000 microliters of liquid per pipetting operation. Thetip includes a buik-in filter that prevents the possibilityof liquid inside the tip entering the pipetting channelhardware.

Plate carrier Carrier for deepwell plate and microweilplate on the instrument.

Reagent reservoir The reagent reservoirs hold thereagents used for sample preparation. The reagentreservoirs are barcoded and are filled manually by theoperator (scan-scan-pour-place principle) for each run.Reagent reservoirs are available in two sizes: 200 mL and50 mL.

Sample carrier Used to bad unprocessed samplesonto and to unload processed samples from theinstrument.


cobas® 4800 System

Scan-scan-pour-placeprinciple - XML Systern Manual

Scan-scan-pour-place principle To minimizehandling errors the reagent reservoirs are filled andplaced using the scan-scan-pour-place principle.

1. Scan the barcode of the reagent vial. 2. Scan thebarcode of the reagent reservoir. 3. Pour the reagent inthe scanned reagent reservoir. 4. Place the filled reagentreservoir onto the reagent reservoir carrier.

Target The DNA or RNA tatget region that is detectedand amplified during PCR.

Teaching needies Eight titanium pipette tips on theinstrument that are used to automatically check of eachpipetting channel. The teaching needies are stored nearthe waste station, next to the tip waste bag.

Thermal block cycler Programmable temperatureblock in the analyzer. The thermal cycler rapidly changestemperature according to the amplification proffie.

Tip rack The tip racks on the instrument holding thedisposable pipetting tips.

Tip rack carrier The tip rack carriers on theinstrument hold the tip racks with the disposablepipetting tips.

UPS Uninterrupted power supply.

XMI Extensible Markup Language.

Roche Diagnostics


Index

cobas® 4800 System

Systern Manual

Index

Index

A

abbreviations, 8alarms— confirming, 132—tab, 131— viewing, 132approvals, 2archiving— parameters, 91— settings, 90—tab, 90audit trail, 81autofilter, 78autoload unit, 43

— overview, 35—x480, 58,64—z480, 68contact addresses, 3context menus, 77control unit, 69controls, specifications, 62conventions used in manual, 7copyrights, 2covers, x 480, 40creating— problem report, 136cross contamination, 22

D

B

barcode reader, handheld, 69barcodes— reading errors, 138basic software elements, 73biohazardous materials, 19block cycler unit, 65buttons— concepts, 75— global action, 75

c

carriers—plates, 55— reagents, 53— stationary, 56— tip racks, 55—x480, 50carryover, 22CFR, 81,82changing— passwords, 92— user accounts, 95circuit breakers, 24cleaning—x480, 105—z480, 115colors in user interface, 74column header context menus, 77columns, displaying and hiding, 77confirming alarms, 132connection errors, 139, 141consumables— for waste, 61

Roche Diagnostics

daily maintenance, for x 480, 105data security, 23database, 81deepwell plates, 59defining— user accounts, 94definitions, see settingsdeleting— user accounts, 95detection unit, 65dimensions—x480, 62—z480, 67disabling tests, 89displaying— columns, 77—flags, 134disposing— analyzer, 27—fluidwaste, 108, 114—waste, 19document information, 2dust filters, 119

E

editing, see changingedition notice, 2electrical safety, 18enabling tests, 89environmental conditions—x480, 62—z480, 68errors— connecting, 139, 141— reading barcodes, 138


Index cobas® 4800 System

Systern Mcrnual

evaporation of samples, 21exchanging—fusesonz480, 122—ventilation dust filters on z 480, 119—xenon lamp on z 480, 116explosion, safety, 20exporting— support data, 97

F

filtering information— advanced features, 79— autofilter, 78— drop-down list, 78filters, for dust, 119fire, safety, 20flags— displaying, 134fluid waste, disposing, 108, 114fuses— exchanging on z 480, 122— safety, 24

installation, 16—x480, 62instrument approvals, 2instrument deck, x 480, 41intended use, 2interfaces—x480, 63—z480, 68ISWAP, 46

1

labels, 25LEDs—x480, 41—z480, 67LIS, 34LIS statuses, 137lists— advanced filtering, 79— filtering, 79— organizing, 76— sorting, 77— use, 76

M

magnet plate, 57maintenance— daily for x 480, 105—weeklyforx 480, 110—x480, 104—z480, 115managing— passwords, 92— user accounts, 93Manual—version, 2measurements—x480, 62—z480, 68messages, 131—work area, 131microwell plates, 60

0

operating con ditions, 16operator qualifications, 16optical safety, 18overview— cobas 4800 user interface, 73— cobas x 480, 32, 39—cobasz480, 33,65— control unit, 34— system, 31

p

passwords— changing, 92— managing, 92— rules, 96physical dimensions, 67—x480, 62

G

general cleaning—x480, 105—z480, 115global action buttons, 75

H

hardware, 37—x480, 39—z480, 65heater unit, 56heater/shaker unit— specifications, 64hiding columns, 77

Roche Diagnostics


cobas® 4800 System Index

Systern Manual

—z480, 67pipetting arm, x 480, 45plate carriers, 55plates— deepweil, 59— microweli, 60power requirements—x480, 62—z480, 67precautions, 16principles—x480, 62—z480, 68problem reports, 136product names, 9protective equipment, 16

Q

qualifications, 16

R

reading errors, 138reagent carriers, 53reagent reservoirs, 58reagents— carriers, 53remote support, 136, 140replacing—fusesonz480, 122— ventilation dust filters on z 480, 119—waste bags, 107, 111—xenon lamp on z480, 116reporting, 88reports— for problems, 136result counters, 98result flags, see flagsresult icons, 134resuits—accuracy, 16retrieving— problem report, 136reviewing— alarms, 132revision history, 2rules— for passwords, 96— for user accounts, 96run recovery, 140

S

safety

Roche Diagnostics


— biohazards, 19— carryover, 22— data security, 23— disposal of analyzer, 27— disposal of instrument, 27— electrical, 18— electromagnetic fields, 17— explosion, 20— fire, 20— fuses, 24— hot surfaces, 22— incorrect results, 22— labels, 25— labels on the system, 25— moving parts, 20— operating conditions, 16— optical, 18— power failure, 17—precautions, 16— result accuracy, 16—samples, 21—use, 16—waste, 19safety classification, 15sample carriers, x 480, 50samples—safety, 21— specifications, 62sealing film, 60settings, for archiving, 90shaker unit, 56software version, 2sorting list entries, 77stationary carrier, 56support data, 97symbols, 7system— settings cobas 4800, 87

T

tabs— Alarms, 131— Audit trail, 81— Configuration, 87— Export support data, 97— in user interface, 74— Messages, 132— Users, 93— Workpiace, 74taking Out of operation, 141teaching needles, x 480, 46technical specifications—x480, 61—z480, 67tests

151

Index cobas® 4800 System

Systeni Manual

— disabling, 89— enabling, 89third-party software, 17tip rack carriers, 55track positions, x 480, 42trademarks, 2

u

unloading— x 480 manually, 140unlocking user accounts, 95use of manual, 7user accounts—changing, 95— defining, 94— deleting, 95— management, 93—rules, 96— unlocking, 95user interface— colors, 74—lists, 76—tabs, 74user management, 92

—LEDs, 41— maintenance, 104— manual unloading, 140— pipetting arm, 45— sample carriers, 50— teaching needies, 46— technical specifications, 61— track pos itions, 42— waste container, 48— waste station, 47xenon lamp, exchanging on z 480, 116

z

z480, 65— block cycler unit, 65— detection unit, 65— LEDs, 67— technical specifications, 67

1

ventilation dust filters, exchanging on Z 480, 119

w

waste— consumables, 61— emptying fluids, 108, 114— replacing bags, 107, 111—safety, 19—x480, 63waste bags, replacing, 107, 111waste container, x 480, 48waste station, x 480, 47weekly maintenance, for x 480, 110wizards, 80

x

x480, 39— autoload unit, 43— carriers, 50— consumables, 58— covers, 40— heater/shaker unit, 56— instrument deck, 41—ISWAP, 46

Roche Diagnosties


Revisions

Documents

System Manual Software Version 2 - · PDF filecobas® 4800 System Document information Systeni Manual Revision history Instrument approvals Roche Diagnostics 2 Manual version Software