Roche MagNA Pure Compact Instrument Operator's Manual

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Page 1

MagNA Pure Compact Instrument Addendum 5 to Operator’s Manual, Version 1.3

Software Version 1.1 July 2016

For general laboratory use.

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Updated Information about the MagNA Pure Compact System

Dear Valued User of the MagNA Pure Compact System,

Please be informed that Section III, Declaration of Conformity is replaced by the following section:

Approvals

The MagNA Pure Compact System meets the requirements laid down in:

Directive 2014/30/EU of the European Parliament and Council of 26 February 2014 relating to electromagnetic compatibility (EMC).

Directive 2014/35/EU of the European Parliament and Council of 26 February 2014 relating to electrical equipment designed for use within certain voltage limits.

Compliance with the applicable directive(s) is provided by means of the Declaration of Conformity.

The following marks demonstrate compliance:

Complies with the provisions of the applicable EU directives.

Issued by Underwriters Laboratories, Inc. (UL) for Canada and the US.

Equipment de Laboratoire / Laboratory Equipment

‘Laboratory Equipment’ is the product identiﬁer as shown on the type plate.

MagNA Pure Compact Instrument – Addendum 5 to Operator’s Manual, Version 1.3

Page 4

If you have any questions regarding the MagNA Pure Compact System Instrument, please contact your Roche Diagnostics representative.

Published by

Roche Diagnostics GmbH Sandhofer Straße 116 68305 Mannheim Germany

2013 Roche Diagnostics

0805521100110716

For general laboratory use.

MAGNA PURE, LIGHTCYCLER, AND TAQMAN are trademarks of Roche.

Page 5

MagNA Pure Compact Instrument Addendum 4 to Operator’s Manual, Version 1.3

Software Version 1.1 November 2013

For general laboratory use.

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Updated Information for the MagNA Pure Compact Instrument

Dear Valued User of the MagNA Pure Compact Instrument,

This addendum is to inform you that the ﬂoppy disk drive for the MagNA Pure Compact Instruments has been removed for serial numbers starting with MPCC1550.

If you have any questions regarding the MagNA Pure Compact System, please contact your Roche Diagnostics representative. To call, write, fax, or email us, visit the Roche Applied Science homepage at www.roche-applied-science.com and select your home country. Coun- try-speciﬁc contact information will be displayed.

Addendum 4 to Operator’s Manual, Version 1.3

Page 8

Updated Information for the MagNA Pure Compact Instrument

Please note the following correction to the MagNA Pure Compact Operator’s Manual:

The ﬂoppy disk drive on the MagNA Pure Compact Instruments starting with serial number MPCC1550 has been removed.

Old Version New Version without Floppy Disk Drive

MagNA Pure Compact Instrument

Page 9

Updated Information for the MagNA Pure Compact Instrument

The MagNA Pure Compact Operator’s Manual is corrected as shown below:

Section Current Version Changes

A 3.3.1 8 Disk Drive (p 24)

A 3.3.4 Sides of the Instrument (p 29)

B 4 Data Transfer to or from the MagNA Pure Compact Instrument (p 67)

8 Disk Drive The disk drive allows the operator to

store the data generated as well as transfer it easily to other instruments or computers (e.g., for sample tracking, documentation, or troubleshooting).

In addition, new MagNA Pure Compact puriﬁcation protocols can be uploaded from commercially available disks.

9 USB Ports There are two USB ports. USB 1 and

USB 2 ports can be used for any accessories that are not included with the MagNA Pure Compact Instrument.

The data from the result screen can be saved to a disk. In future applications with the LightCycler

System and the COBAS TaqMan® 48 Analyzer, these data ﬁles can be transferred to the respective instruments.

Section 8 Disk Drive no longer valid.

9 USB Ports There are two USB ports. USB 1 and

USB 2 ports can be used for any accessories that are not included with the MagNA Pure Compact Instrument.

A USB memory stick allows the operator to store the data generated or transfer it easily to other instruments or computers (e.g., for sample tracking, documentation, or troubleshooting).

In addition, new MagNA Pure Compact puriﬁcation protocols can be uploaded.

To save data from the result screen, use a USB storage device.

Addendum 4 to Operator’s Manual, Version 1.3

Page 10

Updated Information for the MagNA Pure Compact Instrument

Section Current Version Changes

B 4.2 Upload of New Updated Puriﬁcation Protocols (p 67)

As new or updated puriﬁcation protocols are created, they may be added to the MagNA Pure

Compact Instrument via external data carrier disks (e.g., software update disk) during program startup.

Additional protocols will be available for download from www. magnapure. com. Follow the download instructions on this webpage.

Update disks will automatically be checked for viruses by the instrument software.

Workﬂow:

1. MagNA Pure Compact Instrument must be shut down.

2. Insert update disk.

3. Switch on instrument.

4. Software is automatically updated.

5. After Main Screen is displayed, remove update disk.

6. Update complete.

7. The instrument is ready for use.

To upload new protocols, use a USB storage device.

No longer valid.

Workﬂow:

1. MagNA Pure Compact Instrument must be shut down.

2. Insert USB.

3. Switch on instrument.

4. Software is automatically updated.

5. After Main Screen is displayed, shut down the MagNA Pure Compact Software, remove USB, and start the MagNA Pure Compact Software again.

6. Update complete.

7. The instrument is ready for use.

C 5 Documentation (p 97)

The result screen of the respective run will be displayed and can be printed or saved to a disk or LIMS.

To save data from the result screen, use a USB storage device or save them directly to a LIMS.

MagNA Pure Compact Instrument

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Published by

Published by Roche Diagnostics GmbH Sandhofer Straße 116 68305 Mannheim Germany

2013 Roche Diagnostics

1113

For general laboratory use.

MAGNA PURE, LIGHTCYCLER, AND TAQMAN are trademarks of Roche.

Page 13

MagNA Pure Compact Instrument

Addendum 3 to

Operator’s Manual, Version 1.3

Software Version 1.1 August 2012

For general laboratory use.

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Information regarding MagNA Pure Compact Instrument

Dear Valued User of the MagNA Pure Compact Instrument,

Roche Diagnostics Ltd. has merged into Roche Diagnostics International Ltd and therefore the company name has changed to

Roche Diagnostics International Ltd

In order to harmonize and improve our support, the legal manufacturer changes as follows:

Roche Diagnostics GmbH

Sandhofer Strasse 116 68305 Mannheim Germany

If you have any further questions regarding this matter, please do not hesitate to contact your Roche Diagnostics representative. To call, write, fax, or email us, visit the Roche Applied Science home page, http://www.roche-applied-science.com and select your home country. Country-speciﬁc contact information will be displayed.

The address of the legal manufacturer in section “Prologue/Contact Addresses” changes as follows:

Old adress New adress

Roche Diagnostics Ltd. Forrenstrasse CH-6343 Rotkreuz Switzerland

MAGNA PURE is a trademark of Roche.

Roche Diagnostics GmbH Sandhofer Strasse 116 68305 Mannheim Germany

06845070001 a 0812

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Information regarding the MagNA Pure Compact Instrument Operator’s Manual Version 1.3

Versatile Nucleic Acid Purification -

Smart. Small. Simple

Page 16

MagNA Pure Compact Instrument Operator’s Manual - 2

Addendum

Dear valued user of the MagNA Pure Compact Instrument,

With this document Roche Applied Science releases information on safety standards to provide a maximum of health and environment assurance. Please read the following information carefully, which updates information given in the MagNA Compact Instrument Operator’s Manual.

If you have any further questions regarding this matter, please do not hesitate to contact our Technical Services Department at your best convenience. To call, write, fax, or email us, visit the Roche Applied Science home page, http://www.roche-applied-science.com and select your home country. Country-speciﬁ c contact information will be displayed.

New Prologue Chapters:

Warnings and Precautions

In an emergency, immediately turn the power switch off and unplug the Instrument.

This Instrument is an electromechanical device, that could cause electrical shock or injury if not operated according to the procedures in this Operator’s Manual.

Disposal Recommendations

All electrical and electronic products should be disposed off separately from the municipal waste system. Proper disposal of your old appliance prevents potential negative consequences for the environment and human health.

The Instrument must be treated as biologically contaminated-hazardous waste. Decontamination (i.e., a combination of processes, including cleaning, disinfection and/or sterilization) is required before reuse, recycling, or disposal.

Dispose of the Instrument according to local and/or labor regulations.

For more information, contact your local Roche representative.

Components of your Control Unit, such as the computer, monitor, keyboard etc., which are marked with the crossed-out wheeled bin symbol are covered by the European Directive 2002/96/EC on waste electrical and electronic equipment (WEEE) of the European Parliament and the Council of 27 January 2003.

These items must be disposed of via designated collection facilities appointed by government or local authorities.

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

Constraint

It is left to the responsible laboratory organization to determine whether control unit components are contaminated or not. If contaminated, treat in the same way as the Instrument.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

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MagNA Pure Compact Instrument Operator’s Manual - 2nd Addendum

Symbols used in the Manual, page 8

Current Version

Symbol Heading Description

WARNING RISK OF DANGER

HOT SURFACE This symbol is used to label potentially hot instrument surfaces.

BIOHAZARD This symbol is used to indicate that certain precautions must be taken

IMPORTANT NOTE This symbol is used to bring your attention to an important annotation.

INFORMATION NOTE Designates a note that provides additional information concerning the

This symbol is used to indicate that noncompliance with instructions or procedures may lead to physical injury or even death or could cause damage to the instrument.

when working with potentially infectious material.

current topic or procedure.

Additional Information:

Symbol Heading Description

WEE Electrical and electronic equipment marked with this symbol are covered

by the European directive WEEE.

The symbol denotes that the equipment must not be disposed off in the municipal waste system.

General Information, page 11

Current Version Additional Information

Electrical Safety

General Information: Protection Class I

All peripheral devices that are connected to the MagNA Pure Compact

The MagNA Pure Compact Instrument is designed in accordance

with Protection Class I (IEC). The chassis/housing of the Instrument is connected to protection earth (PE) by means of a cable. For protection against electrical shock hazards, the Instrument must be directly connected to an approved power source, such as a three-wire grounded receptacle for the 230V line. Where an ungrounded receptacle is encountered, a qualiﬁ ed electrician must replace it with a properly (PE) grounded receptacle, in accordance with the local electrical code. An extension must not be used. Any break in the electrical ground path, whether inside or outside the Instrument, could create a hazardous condition. Under no circumstances should the user attempt to modify or deliberately defeat the safety features of this Instrument. If the power cord becomes cracked, frayed, broken, or otherwise damaged, it must be replaced immediately with the equivalent part from Roche Diagnostics.

Instrument must comply with safety standard IEC 60950 for information technology equipment, or with IEC 61010-1, UL 61010-1 for laboratory instruments.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 18

MagNA Pure Compact Instrument Operator’s Manual - 2nd Addendum

Setup, page 16

Current Version Additional Information

Selecting a Location

The MagNA Pure Compact Instrument requires very little setup. Choose for the MagNA

Pure Compact Instrument a clean, dry, level, stable surface within 3 m of a compatible electrical outlet. To ensure proper ventilation, leave 10 cm of space behind the instrument and 15 cm at each side of the instrument. No space is needed at the back of the instrument.

Description of the Instrument, page 22

Current Version Additional Information

UV Light Protection

The door permits a good view of the interior of the instrument. During the decontamination cycle, the door prevents escape of UV light from the interior.

Description of the Instrument, page 29

To carry the instrument, place your hands under the base of the instrument. For this purpose, the instrument base plate provides four recessed carrier grips. The weight of the MagNA Pure Compact Instrument is approx. 60 kg, ensure that enough manpower is available for transportation.

The Front Door is impervious to UV light from inside the Instrument, in case the decontamination function is activated, but permits good view to the inside of the Instrument. However do not look at the UV source directly.

Locking of the door is controlled by the software. Movement of the Robotic Arm is only possible after the Instrument Door is closed and locked.

Current Version Additional Information

Socket for power cable

This is the plug-in for the power cable. There are two power cables included in the instrument package, one for US and one for German wall outlets.

Performing a Puriﬁ cation Run, page 43

Current Version Additional Information

For kit speciﬁ c details regarding the handling of Reagent Cartridges, please see the corresponding pack insert of the kit.

Cleaning, page 81

Current Version Additional Information

The surface of the MagNA Pure Compact Instrument as well as removable internal parts should be cleaned on a weekly basis with a lint free cloth moistened with deonized water. If a spill of reagents occurs, the instrument should be cleaned with a 70% ethanol solution or any acceptable PCR laboratory cleaner. Turn the instrument power Off and disconnect or unplug the power cord before cleaning the instrument.

Always connect the Instrument to a grounded wall outlet.

Reagents might be ﬂ ammable. For kit speciﬁ c details regarding the handling of Reagent Cartridges, please consult the package insert of the respective reagent kit for further information.

Mixtures of water and ethanol, that contain

70% ethanol, are highly ﬂ ammable.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

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Information regarding the MagNA Pure Compact Software Update 1.1.2

Versatile Nucleic Acid Purification -

Smart. Small. Simple

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Information regarding the MagNA Pure Compact Software Update 1.1.2

Please read the following information, which updates information given in the MagNA Pure Compact Instrument Operator’s Manual!

Dear valued user of the MagNA Pure Compact Instrument,

In March 2009, Roche Applied Science introduced an updated version of the MagNA Pure Compact Software: Version 1.1.2.

This latest version:

䉴 ﬁ xes some bugs, found in previous versions

䉴 improves some of the text messages

䉴 updates the start up functions of the instrument, including the Plausibility Check

䉴 improves tip handling

䉴 includes updated and improved protocols; a list of installed protocols has also been

implemented in the Maintenance Menu

䉴 improves Sample Ordering

䉴 includes a Create Problem Report function

Information regarding the MagNA Pure Compact Software Update 1.1.2

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Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Versatile Nucleic Acid Purification -

Smart. Small. Simple

Page 22

Prologue

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Please read the following information, which updates information given in the MagNA Pure Compact Instrument Operator’s Manual!

Prologue

Contact Addresses, page 5

Current Version Changes

Manufactured by Roche Instrument Center AG

Forrenstrasse CH-6343 Rotkreuz Switzerland

Marks of Conformity, page 6

Current Version Changes

The MagNA Pure Compact Instrument has been investigated according to:

CE – Testing Information

EN 61326:1997 + A1:1998 + A2:2001 Class B (“Electrical equipment for measurement, control and laboratory use – EMC requirements”)

CAN/CSA C22.2 No. 1010.1-92 CAN/CSA C22.2 CSA C22.2.61010.1

The instrument conforms to following directives as issued by the European Union according to the Council Directive 89/336/EEC (Electromagnetic Compatibility) and 73/23/EEC (Electrical equipment for use within certain voltage limits).

Roche Diagnostics Ltd. Forrenstrasse CH-6343 Rotkreuz Switzerland

EN 61326:2006 Class B (“Electrical equipment for measurement, control and laboratory use – EMC requirements”)

The instrument conforms to the following directives as issued by the European Union according to the Council Directive 2004/108/EC (Electromagnetic Compatibility) and 2006/95/EC (Electrical equipment for use within certain voltage limits).

Please Note: the sentence “Equipment to be connected must fulﬁ ll the standards set by IEC 950 (Information security in technical equipment, including electronic business machines).”, should be disregarded.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

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Chapter A

Chapter A:

2. Installation of the Instrument

2.4 Setup, page 16

Current Version Changes

2.4.1 Selecting a Location

The MagNA Pure Compact Instrument requires very little setup. Choose for the MagNA Pure Compact Instrument a clean, dry, level, stable surface within 3 m of a compatible electrical outlet. To ensure proper ventilation, leave 10 cm of space behind the instrument and 15 cm at each side of the instrument. No space is needed at the back of the instrument.

3. Description of the Instrument

3.3.5 MagNA Pure Compact Accessories

7 Barcode Scanner – Scanner Speciﬁ cations, page 33

Current Version Changes

Drop Resistance IEC 68-2-32 Test ED; withstands

repeated drops from 1.8 m onto a concrete surface

DIN EN 60068-2-32 Test ED; withstands repeated drops from 1.8 m onto a concrete surface

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

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Chapter B

Chapter B:

1. Handling the MagNA Pure Compact Software

1.1 Starting the MagNA Pure Compact Instrument, page 37

Current Version Changes

New Screenshot

1.1 Starting the MagNA Pure Compact Instrument, page 38

Current Version Changes

New Screenshot

1.2 Overview of Main Menu Screen

Table 4: Overview of menu and submenu structure, page 41

Current Version Changes

Maintenance: Detailed Actions

Maintaining:

Leakage Test

䉴

Counter and Reminder

䉴

Error Log

䉴

O-ring Exchange

䉴

Liquid Waste Discard

䉴

UV Decontamination

䉴

Maintaining:

Leakage Test

䉴

Counter and Reminder

䉴

Error Log

䉴

O-ring Exchange

䉴

Liquid Waste Discard

䉴

UV Decontamination

䉴

Create Problem Report

䉴

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 25

Chapter B

2. Performing a Puriﬁ cation Run, page 45

Current Version Changes

For the MagNA Pure Compact RNA Isolation Kit:

The selection of an appropriate endogenous IC is of high importance when developing a quantitative RTPCR assay. The IC is co-ampliﬁ ed with the target of interest and serves as a control for several factors: differences in initial template concentrations between different samples, sample-tosample variations in the PCR, presence of PCR inhibitors or the extent of any RNA degradation. The advantage of using an endogenous IC is that both internal control mRNA and target mRNA is extracted from cells or tissue and reverse transcribed together. Commonly used endogenous ICs include so-called housekeeping gene mRNAs. (Note that Roche Applied Science offers several LightCycler® Housekeeping Gene Sets for the detection of human housekeeping genes, incl. G6PDH, HPRT, ALAS, and _2-microglobulin.) The level of expression of an appropriate endogenous IC should not vary with the experimental conditions or treatments to be compared.

The selection of an appropriate endogenous IC is of high importance when developing a quantitative RTPCR assay. The IC is co-ampliﬁ ed with the target of interest and serves as a control for several factors: differences in initial template concentrations between different samples, sample-tosample variations in the PCR, presence of PCR inhibitors or the extent of any RNA degradation. The advantage of using an endogenous IC is that both internal control mRNA and target mRNA is extracted from cells or tissue and reverse transcribed together. Commonly used endogenous ICs include so-called housekeeping gene mRNAs. The level of expression of an appropriate endogenous IC should not vary with the experimental conditions or treatments to be compared.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 26

Chapter C

Chapter C:

1. User Maintenance

1.1 Leakage Test, page 72

Current Version Changes

New Screenshot

1.1 Leakage Test, page 73

Current Version Changes

New Screenshot

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 27

Chapter C

1.2.2 O-Ring Exchange, page 77

Current Version Changes

New Screenshot

1.2.2 O-Ring Exchange, page 78

Current Version Changes

New Pictures

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 28

Chapter C

New Pictures

Current Version Changes

New Pictures

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 29

Chapter C

1.2.2 O-Ring Exchange, page 79

Current Version Changes

New Pictures

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 30

Chapter C

2. Service Maintenance, page 81

Current Version Changes

Note: Service Maintenance may only be

performed by a Roche Diagnostics service engineer. Contact your local Roche representant for maintenance assistance and for more details on country-speciﬁ c service contracts.

2. Exchange: Hepa Filter HEPA Filter

Service Maintenance may only be performed by a Roche Diagnostics service engineer. Contact your local Roche representative for maintenance assistance and for more details on countryspeciﬁ c service contracts.

3. Cleaning Instructions and UV Decontamination

3.2 UV Decontamination, page 85

Current Version Changes

New Screenshot

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 31

4. Error Codes and Trouble Shooting Guide

4.1 Error Log, page 86

Current Version Changes

Important Note: In case you want to trouble shoot

an error together with a local Roche representant, have these informations ready or make sure the remote service option is enabled.

New Screenshot

In the event that you want to trouble shoot an error, together with a local Roche representative, have this information ready, or ensure that the remote service option is enabled.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 32

Chapter C

6. Administrator Authorization, page 98

Current Version Changes

Your local Roche Diagnostics representant will deﬁ ne an administrator authorization during instrument installation. The administrator rights are secured with a password and enable to deﬁ ne additional operators. During the administrator authorization the password will be displayed hidden, to guarantee conﬁ dentiality. In case you should forget the administrator password, contact your local Roche Diagnostics representant and you will receive a new one.

Your local Roche Diagnostics representative will deﬁ ne an administrator authorization during installation of the Instrument. The administrator rights are secured with a password and enable the ability to deﬁ ne additional operators. During the administrator authorization the password will be displayed hidden, to guarantee conﬁ dentiality. In the event that you forget the administrator password, contact your local Roche Diagnostics representative and you will receive a new one.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 33

Chapter C

7. Ordering Guide

7.1 Related Products, page 99

Current Version Changes

Recommended Printer for Use with the MagNA Pure Compact Instrument:

Hewlett Packard Laserjet 1015 Please contact your local Roche

representative for details.

For installation with the MagNA Pure Compact Instrument, please contact your local Roche representantative.

For installation with the MagNA Pure Compact Instrument, please contact your local Roche representative.

7.3 MagNA Pure Compact Accessories, page 100

Current Version Changes

Waste Tank 03 788 270 001 03 788 300 001

Drop Catcher 03 788 300 001 03 788 270 001

Trademarks MAGNA PURE, LIGHTCYCLER,

COBAS, and TAQMAN are trademarks of Roche.

MAGNA PURE, LIGHTCYCLER, LC, HYBPROBE, COBAS and TAQMAN are trademarks of Roche.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 34

Additional Information

Chapter C:

1. User Maintenance

1.3 Create a Problem Report

For troubleshooting by a Roche representative, error messages and conﬁ guration ﬁ les can be exported to a Problem Report.

The Problem Report is a zipped ﬁ le containing log, conﬁ guration and version ﬁ les.

To create a Problem Report:

Insert an empty USB Memory Stick on the right side of the Instrument. On the “Main Menu”

screen, press the ‘Maintenance’ button. Press the ‘Create Problem Report’ button and select “OK” in the pop-up window.

The Problem Report is created and stored on the attached USB Memory Stick. A pop-up window

will open when the Problem Report has been saved.

1. User Maintenance

1.3 Show All Protocols

The “Show All Protocols” option lists all the protocols which are installed on the MagNA Pure Compact Instrument.

To “Show All Protocols”

On the “Main Menu” screen, press the ‘Maintenance’ button. Select the “Show All Protocols”

button.

All protocols that are installed on the Instrument will be displayed, as shown in the screenshot

below.

Important Information regarding the MagNA Pure Compact Instrument Operator’s Manual

Page 35

MagNA Pure Compact Operator’s Manual

Instrument Version 1.0 Software Version 1.1

www.roche-applied-science.com

Page 36

Page 37

Table of Contents

Prologue Page

Intended Use of the Instrument...................................................................................................................5

Contact Adresses....................................................................... .............................................................................5

Revision History.................................................................... ....................................................................................5

Marks of Conformity..............................................................................................................................................6

How to Use this Manual....... ................................................................................................................................7

Symbols used in the Manual...............................................................................................................................8

A General Overview Page

1. Specification of the Instrument.................................................................................................................11

1.1 General Information................................................................... ...........................................................................11

1.2 Operating Environment.......................................................................................................................................12

1.3 Operating Parameters........................................................ ..................................................................................12

2. Installation of the Instrument.....................................................................................................................13

2.1 Shipping....................................................................................................................................................................13

2.2 Unpacking................................................................................................................................................................13

2.3 Additional Items Required for Operation and Maintenance................................................................. 14

2.3.1 Operating Reagents......................................................................................................................................14

2.3.2 Maintenance Items......................................... ..............................................................................................15

2.4 Set-up........................................................................................................................................................................16

2.4.1 Selecting a Location.....................................................................................................................................16

2.4.2 Easy Teaching Procedure.............................. ..............................................................................................16

2.4.3 Software Setup...............................................................................................................................................17

3. Description of the Instrument....................................................................................................................21

3.1 General Description..............................................................................................................................................21

3.2 Function Principle..................................................................................................................................................21

3.3 Description of the Instrument...........................................................................................................................22

3.3.1 Front View of the Instrument.....................................................................................................................22

3.3.2 Detailed View..................................................................................................................................................25

3.3.3 Back View of the Instrument.....................................................................................................................27

3.3.4 Sides of the Instrument...............................................................................................................................28

3.3.5 MagNA Pure Compact Accessories.. ............................................................................. ........................30

3.3.6 Position and Meaning of Warning Labels............................................................................................34

Page 38

Table of Contents

B How to Operate the MagNA Pure Compact Instrument Page

1. Handling the MagNA Pure Compact Software..................................................................................37

1.1 Starting the MagNA Pure Compact Instrument ...................... ..................................................................37

1.2 Overview of Main Menu Screen..................................................................................................................... 39

1.3 Flow Diagram for Preparation of a Purification Run................................................................................42

2. Performing a Purification Run.....................................................................................................................43

2.1 Purification..............................................................................................................................................................46

2.2 Liquid Waste Discard..........................................................................................................................................62

3. Use of Internal Controls................................................................................................................................66

3.1 Function of Internal Control................................... ...........................................................................................66

3.2 How to program the instrument for an internal control......................................................................... 66

4. Data Transfer to or from the MagNA Pure Compact Instrument............................................67

4.1 Data Transfer to other Instruments........ ............................................................................. ............................67

4.2 Upload of New or Updated Purification Protocols....................................................................................67

C Maintenance and Trouble Shooting Page

1. User Maintenance............................................................................................................................................ 71

1.1 Leakage Test ......................................................................................................................................................... 71

1.2 O-ring Maintenance.............................................................................................................................................75

1.2.1 Greasing the O-rings....................................................................................................................................75

1.2.2 O-ring Exchange................................................ ............................................................................................76

2. Service Maintenance......................................................................................................................................81

2.1 Counter and Reminder.................................................................................. ......................................................82

2.2 Remote Control and Host...................................................................................................................................82

3. Cleaning Instructions and UV Decontamination .............................................................................83

3.1 Cleaning....................................................................................................................................................................83

3.2 UV Decontamination............................................................................................................................................85

4. Error Codes and Trouble Shooting Gui de ............................................................................................ 86

4.1 Error Log....................................................................... ...........................................................................................86

4.2 Instrument Error Codes.......................................................................................................................................87

4.3 Trouble Shooting Guide...................................................................................................................................... 94

5. Documentation................................................................................................................................................... 96

6. Administrator Authorization....................................................................................................................... 98

7. Ordering Guide .................................................................................................................................................. 99

7.1 Related Products................................................................................................................................................. 99

7.2 MagNA Pure Compact System Products...................................................................................................100

7.3 MagNA Pure Compact Accessories............................................................................................................100

MagNA Pure Compact Operator’s Manual - Version 1.3

Page 39

Prologue

Page 40

MagNA Pure Compact Operator’s Manual - Version 1.3

Page 41

Intended Use of the Instrument

Contact Addresses

Prologue

Intended Use of the Instrument

The MagNA P ur e C ompact I nstrument is a r obotic w orkstation f or the aut o mat ed pr eparation of nucleic acids from a broad variety of sample materials (e.g., mammalian blood, serum, plasma, or blood cells; cultured cells; tissue) with the assistance of specially designed MagNA Pure Compact reagent kits. The isolated high-quality nucleic acids are suitable for PCR and RT-PCR reactions on the LightCycler System, as well as on standard block cyclers, and for many other downstream applications.

The instrument is intended for nucleic acid preparation in general laboratory use by trained professionals.

Contact Addresses

Manufactured by Roche Instrument Center AG

Forrenstrasse CH-6343 Rotkreuz Switzerland

for Roche Diagnostics GmbH

Sandhofer Straße 116 D-68305 Mannheim Germany

Distribution in USA Roche Diagnostics Corporation

9115 Hague Road PO Box 50457 Indianapolis, IN 46250 USA

Revision History

Manual Version

1.1 1.0 1.0 December 2003

1.2 1.0 1.1 August 2004

1.3 1.0 1.1 February 2006

Instrument Version

Software Version

Revision Date

Prologue

Page 42

Intended Use of the Instrument

Marks of Conformity

The MagNA Pure Compact Instrument had been investigated according to:

䉴 IEC 61010-1, 2nd Edition ("Safety requirements for electrical equipment for

measurement, control and laboratory use; Part 1: General requirements")

䉴 EN 61326:1997 + A1:1998 + A2:2001 Class B ("Electrical equipment for measurement,

control and laboratory use - EMC requirements")

䉴 UL 61010A-1 䉴 CAN/CSA C22.2 No. 1010.1-92

The instrument has been manufactured and checked in accordance with all relevant safety standards prior to leaving the factory. The instrument has been app ro v ed for use by recognized testing institutions. This is confirmed by the following conformity symbols:

Acronym Test Symbol Testing Information

CE The instrument conforms to following directives as

CUL Certified by the Underwriters Laboratories Inc.

issued by the European Union according to the Council Directive 89/336/EEC (Electromagnetic Compatibility) and 73/23/EEC (Electrical equipment for use within certain voltage limits).

Equipment to be connected must fulfill the standards set by IEC 950 (Informationsecurity in technical equipment, including electronic business machines).

Classification Note on Use with Infectious Material

The Instrument is classified as: 䉴 The Instrument may not be used to

analyze

䉴 Designed for stationary operation. 䉴 Intended f or worldwide use. 䉴 Intended for evaluating preprocessed

infectious materials unless additional safety measures to ensure safe sample handling are taken beforehand.

biological material.

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How to Use this Manual

Important: Before operating the MagNA Pure Compact Instrument, be sure to read and

understand the warnings, cautions and safety requirements in this manual. Failure to follow the instructions contained in this manual may hav e hazardous consequences.

Chapter A General Overview describes

䉴 contents of the MagNA Pure Compact system package 䉴 design of the instrument 䉴 accessories and disposable plastics required for instrument operation 䉴 isolation method of the MagNA Pure Compact Instrument

Intended Use of the Instrument

How to Use this Manual

Chapter B How To Operate the MagNA Pure Compact Instrument describes how to

䉴 use the MagNA Pure Compact Software 䉴 prepare the instrument for a purification run 䉴 perform a purification run

Chapter C Presents additional information on maintenance

of the instrument and troubleshooting

䉴 User Maintenance 䉴 Service Maintenance by the Roche service 䉴 Cleaning of the instrument 䉴 Troubleshooting

Prologue

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Intended Use of the Instrumentl

Symbols used in this Manual

Symbol Heading Description

WARNING RISK OF DANGER

HOT SURFACE This symbol is used to label potentially hot

BIOHAZARD This symbol is used to indicate that certain

IMPORTANT NOTE This symbol is used to bring your attention to

INFORMATION NOTE Designates a note that provides additional

This symbol is used to indicate that noncompliance with instructions or procedures may lead to physical injury or even death or could cause damage to the instrument.

instrument surfaces.

precautions must be taken when working with potentially infectious material.

an important annotation.

information concerning the current topic or procedure.

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General Overview

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Specifications of the Instrument

General Information

General Overview

1 Specifications of the Instrument

Do not use the equipment in a manner not specified by the manufacturer . Otherwise, the protection provided by the equipment might be impaired.

1.1 General Information

Cat. No. Dimensions Weight Power supply Frequency 50/60 Hz +/- 5% Power consumption Fuses Heat emission

Protection Class Installation Category Electromagnetic Emission: Terminal disturbances voltage Electromagnetic radiation

disturbances

03 731 146 001 W 540 mm; D 610 mm; H 570 mm approx. 60 kg 100 - 240 V AC +/- 10%

Max. 400 VA

4.0 AT, 2 pieces 1440 kJ/h (max.)

860 kJ/h (average value during operation) I

Class B Class B

General Overview

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Specifications of the Instrument

Operating Environment

1.2 Operating Environment

Temperatures allowed during transportation/storage/packaging

Temperatures allowed during operation

Pollution Degree: 2 Maximum relative humidity

Altitude

1.3 Operating Parameters

Note: Exact values depend on the purification protocol used.

Processing capability Processing time Pipetting Accuracy

-25°C to +70°C

+18°C to +30°C

Indoor use 80% (for operating temperatures up to 31°C);

decreases linearly to 50% for operating temperatures up to 40°C

up to 2000 m

1 to 8 samples per batch 20 to 45 min (depending on protocol) 25 µl to 100 µl: ⱕ5%

⬎100 µl ⱕ2%

Sample Volume Elution Volume Internal Control Volume

100 – 1000 µl 50 – 200 µl 5 – 20 µl

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Installation of the Instrument

Shipping

2 Installation of the Instrument

2.1 Shipping

The MagNA Pure Compact Instrument is shipped in a styrofoam container surrounded by a cardboard box. Before opening it, inspect the container carefully for damage. Report any damage to your local Roche Diagnostics office before accepting the unit.

2.2 Unpacking

Note: The following steps will be done by your local Roche Diagnostics representative.

Standard Component List

䉴 1 MagNA Pure Compact Instrument body

Individual parts:

䉴 1 Cartridge Rack 䉴 1 Tube Rack 䉴 1 Elution Tube Rack 䉴 1 Waste Tank 䉴 1 Drop Catcher 䉴 1 Drip Tray 䉴 1 Barcode Scanner and cable 䉴 US power cable 䉴 German power cable 䉴 1 package High Vacuum Grease 䉴 1 package O-rings (8 pieces) 䉴 2 fuses for line filter 䉴 Operator’s Manual

The MagNA Pure Compact Instrument is a standalone instrument, which needs no additional computer. The computer is already included in the instrument housing and and may be operated via a touch-screen.

General Overview

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Installation of the Instrument

Additional Required Items for Operation and Maintena nce

2.3 Additional Items Required for Operation and Maintenance

2.3.1 Operating Reagents

Before operating the MagNA Pure Compact Instrument for the first time, you must have one of the following reagen t k its:

Cat. No. Purific ation Kit For Preparation Of

03 730 964 001 MagNA Pure Compact Nucleic

Acid Isolation Kit I

03 730 972 001 MagNA Pure Compact Nucleic

Acid Isolation Kit I - Large Volume

04 802 993 001 MagNA Pure Compact

RNA Isolation Kit

These three kits for the purification of genomic DNA, viral total nucleic acid (DNA and RNA) or total RNA are currently available from Roche Diagnostics. The instrument software already contains operating protocols that can be used with Nucleic Acid Isolation Kits. Purification protocols for the MagNA Pure Compact RNA Isolation Kit are available for download from http://www.roche-applied-science.com/sis/ magnapure/magna_compact_protocols.htm. Please contact your local Roche representative or visit www.magnapure.com for the latest information on additional purification kits and protocols. See section 4.2 for details on how to install new purification protocols into the MagNA Pure Compact software.

Each purification kit includes the reagents and disposables needed for a standard purification run. If you need additional tubes, e.g. for an internal control or maintenance activities (leakage test), you must order them from Sarstedt. (See the Appendix for detailed ordering information.)

Genomic DNA from mammalian whole blood, plasma and culture cells. Total nucleic acids from mammalian plasma and whole blood.

Total RNA from mammalian whole blood, blood cells, cultured cells, and tissue.

the MagNA Pure Compact

Note: The actual amount of reagents and disposables may vary between the different

available MagNA Pure Compact purification kits.

Kit content:

䉴 Prefilled Reagent Cartridges (individually packed in a sealed foil pouch, with barcode)

䉴 Sample Tubes (35 tubes per package, 2.0 ml each, with stand, without barcode)

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Installation of the Instrument

Additional Required Items for Operation and Maintenance

Kit content:

䉴 Elution Tubes (35 tubes per package, 2.0 ml each, with stand, with barcode)

䉴 Caps for Elution Tubes (35 caps per caps)

䉴 Tip Trays (including Piercing Tool and tips). The tips are placed in the following order

into the Tip Tray: one Piercing Tool, one small tip, two large tips.

2.3.2 Maintenance Items

Cat. No. Purification Kit Contents

03 561 429 001 MagNA Pure LC O-Ring Maintenance Kit O-rings (12 x 8),

High Vacuum Grease (1)

03 753 166 001 MagNA Pure Compact Tip Tray Kit 10 Tip Trays

Note:

䉴 To ensure that they work correctly, you must grease the O-rings once per week (or

after every 20 purification runs). If the O-rings malfunction, the instrument nozzles may leak. For details, please see the Maintenance section in Chapter C.

䉴 Perform a leakage test every two months (or after every 50 purifi cation runs) to deter-

mine whether the O-rings should be changed. For details please see the Maintenance section in Chapter C.

There is an O-Ring Exchange Tool available, which simplifies the O-ring changing process. Please contact your local Roche Diagnostics representative if you need O-rings changed or want one of these tools.

General Overview

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Installation of the Instrument

Setup

2.4 Setup

2.4.1 Selecting a Location

The MagNA Pure Compact Instrument requires very little setup. Choose for the MagNA Pure Compact Instrument a clean, dry, level, stable surface within 3 m of a compatible electrical outlet. To ensure proper ve ntilation, lea ve 10 cm of space behind the in strument and 15 cm at each side of the instrument. No space is needed at the back of the instrument.

Protect the MagNA Pure Compact Instrument from heat and excessive sunlight and always ventilate the r oom well. The instrument is for „indoor use only“ and should not be operated in areas of excessive humidity or extremes of temperature. Do not use the instrument where there is a risk of explosion.

2.4.2 Easy Teaching Procedure

The software has been preinstalled by the manufacturer. The installer (service user) must perform an adjustment procedure, called Easy Teaching, before the instrument can be used. Only a service operator, not a regular operator, can access the menu for the Easy Teaching procedure. This is done by your local Roche Diagnostics representative.

Note: The Easy Teaching Procedure must be performed before the instrument will work

correctly. If the adjustment is not done pr operly, either the instrument could be damaged or the instrument performance could be affected (e.g. pipetting accuracy, y ield in nucleic acids, etc.).

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Installation of the Instrument

Setup

2.4.3 Software Setup

Either a service operator or a regular operator can access the menu for software setup. This menu enables the operator to

䉴 set the time and date 䉴 preset the location (folder) where all generated data will be sav ed 䉴 enter a laboratory name 䉴 choose the types (and loudness) of alarm sounds the instrument will generate 䉴 manage the list of operators that have access to the instrument 䉴 specify the types of sample materials to be handled with the instrument

Note: The type of sample material used for a purification run can be selected later on

during Sample Ordering 2 (see chapter B for details). It is used for documentation purposes only and does not influence the purification protocol.

Action Software Screen

Turn on the MagNA Pure Compact Instrument by pressing the Power On button

on the front of the instrument. During initialisation/self test of the system components the start-up screen

appears. The MAIN MENU Screen appears

Touch the SETUP Button on the touch-screen

The SETUP Screen appears

Note: Touch the Back button

(at the lower right corner of the SETUP Screen) to return to the MAIN MENU Screen.

Touch the SETTINGS Button

The SETTINGS Screen appears.

Note: Touch the Back button (at the lower right corner of the SETTINGS Screen)

to return to the SETUP Screen without changing any of the current settings.

General Overview

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Installation of the Instrument

Setup

Action Software Screen

Basic Settings

Program the actual time and date by pressing the buttons next to the time and date displays. A pop up window opens to allow you to set the correct values.

Touch the Up and Down buttons (to the right of each number) to change the values for hours and minutes (see figure). The Up button increases values by one unit, the Down button decreases values by one unit. Touch the OK button to confirm the changes and return to the SETTINGS Screen. Touch the Cancel button to return to the Settings Screen without changing any settings.

Note: The hour setting uses a 24-hour clock, where 11:00 PM is hour 23, and

midnight is hour 0. The hour and minute values can be set independently; that is, you can change from minute 59 to minute 0 (or vice versa) without causing the hour setting to change.

Touch the Up and Down buttons (to the right of each number) to change the values for year, month and day (see figure). The Up button increases values; the Down button decreases values. Touch the OK button to confirm the changes and return to the SETTINGS Screen. Touch the Cancel button to return to the SETTINGS Screen without changing any settings.

Note: These values can be set independently . You can change from December to

January (or vice versa), without causing the year to change. Y ou can change from day 30 (or 31) to day 1 (or vice versa) without causing the month to change.

To specify the default folder where all generated data will be saved, touch the Folder field, then use the pop-up virtual keyboard to type the name of the folder into the field .

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Action Software Screen

To specify the default laboratory name that will be mentioned with all generated data, touch the Laboratory Name field, then use the pop-up virtual keyboard to type the laboratory name into the field.

Installation of the Instrument

Setup

Alarm Settings

To specify the types of alarm that the instrument software should give, as well as the loudness of each alarm, touch appropriate buttons on the "Acoustic Signals“ panel.

Note: You can choose to sound an alarm each time an error message is displayed (Error), each time a button has been touched on the virtual keyboard (Keyboard), and each time the purification run has ended (End of the run). If you don’t want one of these alarms, just select for that particular alarm. For each alarm you want, choose whether the alarm sound should be given at low, medium or high volume.

Select Back to return to the Settings Menu without modification.

Select the Operator List button from the Setup menu.

General Overview

To enter a new operator type a new name into the entry field below the Operator List and select the Add button.

Note: Only an administrator can define a new user. The administrator is asked for

his admin password when this button is used. If no administrator should be defined, set the first time the Return key.

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Installation of the Instrument

Setup

Action Software Screen

Select the Material List button from the Setup menu.

To enter a new type of sample material type a new name into the entry field below the material list.

Select the Add button to add the new name to the Material List.

The MagNA Pure Compact Instrument is now ready for use.

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Description of the Instrument

General Description

3 Description of the Instrument

3.1 General Description

The MagNA Pure Compact Instrument is a robotic workstation that can automatically isolate nucleic acids from crude sample material. It is a compact benchtop instrument with an integral touch-screen computer. The central processing unit of the instrument is a robotic arm with an 8-nozzle pipette head. This pipette head can process 1–8 samples per run. In addition, this pipette head has a specialized sensor unit, which can detect clots in sample material and loss of reaction tips.

3.2 Function Principle

When it is purifying DNA, the basic operations of the instrument are:

General Overview

For details on the purification kits (provided in prefilled cartridges) please refer to their pack inserts. All kit pack inserts can be obtained at the Roche home page: http://

www.roche-applied-science.com

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Description of the Instrument

3.3 Description of the Instrument

3.3.1 Front View of the Instrument

1 Housing

Painted sheet metal housing contains the main body of the instrument and protects it from electromagnetic influences, chemicals, and UV-light.

2 Front Door

The nozzle head can only be moved after the instrument door is closed and locked. This door lock is controlled by the software. This prevents anyone from reaching inside the instrument during the purification, which might lead to injuries.

The door permits a good view of the interior of the instrument. During the decontamination cycle, the door prevents escape of UV light from the interior. It also protects reagents, disposable plastics and samples from environmental contamination.

The front door has to be opened to get access to the liquid waste tank and drip tray.

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Description of the Instrument

3 Nozzle Head

The nozzle head moves over the processing stage up and down (vertically along the zaxis). It carries the pipetting unit, the sensor unit and the magnet unit. The pipetting unit consists of 8 independent working air-filled plungers, each connected to a nozzle (1) which takes up the Reaction Tip. The Reaction Tip (3) is held by the O-ring (2) on the nozzle. A specially designed sensor unit checks all 8 channels indiviually for clots in the sample material, correct position of the reagent cartridge and piercing tool, loss of reaction tips, as well as for the presence of sample tube and internal co ntrol tube (if appropriate).

4 Processing Stage

The processing stage holds the cartridge rack with the reagent cartridges, the tip trays, the tube rack with elution tube rack, the heating units and the waste tank. It moves back and forth (horizontally along the y-axis), thereby moving the cartridge rack with the prefilled reagent cartridges into position so they can be processed. It contains a loading mechanics that lifts the cartridge rack to the top position for easy insertion and removal of the cartridge rack or the cartridges. The equipped cartr idge ra ck is then manually pushed down to the low position of the loading mechanics inserting the respective cartridge wells into the heating unit.

5 Touch-screen

From the touch-screen, you can operate all instrument features. E.g., you can program a run, install a new protocol, maintain the instrument or search for accumulated data. You can activate the functions on the touch-screen either with your fingertips or with a PDM pencil.

General Overview

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Description of the Instrument

6 Buttons for Setting Screen Contrast

By pressing the + and – buttons, you can set the brightness of the touch screen.

7 Status Indicator LEDs and Power On Button

The instrument is turned on pressing the "power on" button. Three LEDs indicate the current status of the instrument:

䉴 The green LED of the "power on" button indicates that the instrument is powered on 䉴 the red "processing" LED indicates the status of processing 䉴 the yellow "run c ompleted" LED signalizes that the run is completed.

8 Disk Drive

The disk drive allows the operator to st ore the data generated as well as transfer it easily to other instruments or computers, e.g for sample tracking, documentation or troubleshooting. In addition, new MagNA Pure Compact Purification protocols can be uploaded from commercially available disks.

9 Barcode Scanner

The barcode scanner enables the use of barcodes to track samples through the entire purification process as well as prior (sample preparation) and subsequent steps (e.g. PCR, storage of the eluate). Moreover, when you scan the cartridge barcode, the touchscreen will display the name of the correct MagNA Pure Compact Purification Kit and the instrument will automatically load the appropriat e purificatio n protocol.

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3.3.2 Detailed view

Description of the Instrument

1 Nozzle Head

The nozzle head performs all pipetting steps. Its 8 nozzles can hold up to 8 reaction tips per time. It also contains the tip-loss & clot-detection system (pressure sensor).

2 Magnet Unit

The magnet unit contains permanent magnets and can move forward and backward from the rear of the chamber. For separation of magnetic beads from the buffers, the magnetic plate moves closer to the reaction tips, thereby immobilizing the magnetic beads on the inner surfaces of the reaction tips. The distance between magnet and reaction tips is controlled by the software. The magnet unit also holds the drop catcher .

General Overview

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Description of the Instrument

3 Heating Block

The heating block has two independantly working units for two dedicated wells (for the lysis and elution step) per one reagent cartridge. These wells are separated from each other and from the wells with ambient temperature by a little distance.

4 Tip Rack

The tip rack holds up to 8 Tip Trays, each carrying 2 large tips, 1 small tip, and a disposable piercing tool, which pierces the aluminum foil on every cartridge well before purification starts. After it uses them, the instrument places the tips back into their original positions on the tip tray for easy disposal.

5 Front Door

The front door can be opened for maintenance purposes or to remove the trays, the liquid waste tank, or the drip tray. It is opened by moving the lever at the right door side to the left.

Instrument parts 6-11 are accessories and are described in detail under section 3.3.5 MagNA Pure Compact Accessories.

6 Drop Catcher 7 Cartridge Rack 8 Tube Rack 9 Elution Tube Rack 10 Waste Tank 11 Drip Tray

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Description of the Instrument

3.3.3 Back View of the Instrument Description of Instrument Backmber Instrument Part Description

1 Exhaust fans with HEPA filter

The housing is cooled by air. The instrument has air inlets with dust filters on both sides of the instrument. An exhaust fan expels this air from the back of the instrument through a HEPA (glass fiber) filter.

Note: This HEPA filter retains some aerosols. However, the MagNA Pure Compact

Instrument is not guaranteed to be fully air-tight. Although the total air flow from the platform goes through the HEPA filter , air does flo w unde r the platform as well as ov e r it. Thus, there is a possibility that some of the air surrounding the platform will escape from the instrument without HEPA filtration.

General Overview

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Description of the Instrument

3.3.4 Sides of the Instrument

Description of Right Side of Instrument

1 Air Inlet

Air inlet for electronic compartment, with dust filter.

2 Air Outlet

Air outlet for electronic compartment.

3 Main Switch

Use the Main Switch t o turn the instrument on and off, e.g. in case of an emergency or if the instrument is not in use for longer time periods. In routine daily use the instrument should be turned off via the software button on the touch-screen as described in chapter B.

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Description of the Instrument

4 Socket for power cable

This is the plug-in for the power cable. There are two power cables included in the instrument package, one for US and one for German wall outlets.

5 Fuse

Next to the power inlet is a socket for the 2 main fuses. In case the fuses need to be replaced, make sure to first unplug the instrument from electrical power. A set of spare fuses is enclosed with the instrument.

6 Barcode Scanner port

The PS/2 port marked „Barcode Scanner“ is to be used for the barcode scanner.

7 Parallel Port

The parallel port is intended to be used for the connection with a local printer.

8 Serial Port (RS232)

The serial port might be used for additional external devices for LIMS.

9 USB Ports

There are two USB ports, USB 1 and USB 2 port, can be used for any accessories that are not included with the MagNA Pure Compact Instrument.

Description of Left Side of Instrument

General Overview

1 Air Inlet

Air Inlet for the processing area with dust filter. Dust filters keep dust particles away fr om the inside of the instrument. Air is expelled by a fan through the HEPA filter on the backside of the instrument.

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Description of the Instrument

3.3.5 MagNA Pure Compact Accessories

All MagNA Pure Compact Accessories described below can be ordered separately. For ordering information see chapter C, Orderi ng Guide.

1 Cartridge Rack

The cartridge stage holds the cartridge rack, where the individual prefilled reagent/processing cartridges (up to 8 per purification run) are inserted. The Cartridge Rack can be equipped in and outside of the instrument.

2 Tube Rack

In row 1, the Tube Rack holds up to 8 sample tubes (capacity 2.0 ml), which are provided with the purification kits. If you are running an Internal Control, you can purchase up to 8 additional sample tubes (capacity 2.0 or 1.5 ml) from Sarstedt and place them in row 2 (the Internal Control T ube Rack). (For details see the Related Products section in Chapter C). In row 3, primary sample tubes (not provided) may be placed prior to starting the purification process. To discriminate it from row 1 and 2 the positions of row 3 have a wider diameter.

The rack has numbered positions (1-8) and can stand upright on e.g. a bench. The tubes can be screwed down with one hand, as they are secured against turning by a mechanical anti-twist device.

Note: To ensure correct pipetting, use only these recommended types of tubes for the

Internal Control: 2.0 ml Sarstedt Tubes (without cap: Sarstedt #72.608; with cap: Sarstedt #72.693).

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Description of the Instrument

3 Elution Tube Rack

The Tube Rack also contains a separate rack for elution tubes. The Elution Tube Rack will sit on the tube rack, after both have been equipped. The two holes of the Elution Tube Rack match with the two pins of the tube rack. After assembly the elution tube rack hides the row for primary sample tubes. The elution tube rack holds up to 8 tubes (capacity 2.0 ml), each labelled with an individual barcode. These tubes are provided with the reagent kits. The rack has numbered positions (1-8) and can stand upright on e.g. a bench.

4 Drip Tray

The Drip Tray keeps any accidentally spilled liquid away from the interior of the instrument housing, especially from the electrical components of the instrument which are located below the Processing Stage. It can be removed for cleaning. (For details see the Maintenance section in chapter C.) See chapter C for details on cleaning the drip tray.

General Overview

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Description of the Instrument

5 Waste Tank

The instrument contains an integral waste tank, where liquid waste accumulates during each purification run. It can hold all the liquid waste from one purification run.

Note: To avoid contamination, always remember to empty the waste tank after every

purification run. The tank is located beneath the tube racks, which must be removed before you can reach the tank. The waste tank sensor will determine whether the tank is inserted correctly or not. See chapter C for details on emptying the liquid waste tank.

6 Drop catcher

The drop catcher is carried by the upper side of the magnet unit and is placed directly below the nozzle head each time it moves anywhere except from one well to the next. If a drop should leave the pipet, it is caught by the drop catcher.

The drop catcher can be removed from its place for cleaning purposes. See chapter C for details on possible causes and how to avoid.

7 Barcode Scanner

The barcode scanner is intended for protocol selection (automatically when the kit cartridge is scanned) and positive sample tracking.

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Scanner Specifications

Description of the Instrument

Power Supply Consumption Max. Resolution Scan Rate Min. Print Contrast Ratio Reading Angle

Reading Indicators

Readable Barcodes

Enhanced Features Weight Case Material Cable Length

5 VDC ±5% 250 mA operating, 330 mA max.; 250 µA sleep mode

0.076 mm (3 mils) 270 scans/sec. 15% Skew: ±80°, Pitch: 65°, Tilt ±35° (EAN13, M=0.8,

PCS=0.9) Good Read LED, „green spot“ on the code, adjustable

tone „beeper“ 2/5 family, Code 39 (plus Code 32, Cip 39), EAN/UPC,

EAN 128, Code 128, Code 93, CODABAR, TELEPE N, PLESSEY, Code 49, Code MSI, Code Delta IBM, Code 11, CODABLOCK, and Code 16K, PDF 417

Puzzle SolverTM, data editing and data concatenation (approx.) 200 g ABS and Polycarbonate 2 m (6.1 ft.) linear or coiled

Ambient Light Conditions MTBF Operating Temperatures Storage Temperature Humidity Drop Resistance

ESD Protection Environmental Protection

Up to 100.000 lux >240,000 hours (MIL-HDBK-217F ground benign) 0 to 55 °C

-20 to 70 °C 90% non-condensing IEC 68-2-32 Test ED; withstands repeated drops from

1.8 m onto a concrete surface 16 kV IP30

General Overview

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Description of the Instrument

3.3.6 Position and Meaning of Warning Labels

No. Symbol Location Meaning

Heating Block The hea ting block reaches temperaturs of 100°C. Do not touch the

Housing Biological hazardous material is processed inside the instrument.

Warning Read the Operator's Manual before using the instrument.

block during and directly after purification. If you touch the block, it may burn you.

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How to Operate the MagNA Pure Compact Instrument

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Handling the MagNA Pure Compact Software

Starting the MagNA Pure Compact Instrument

How to Operate the MagNA Pure Compact Instrument

1. Handling the MagNA Pure Compact Software

Once the MagNA Pure Compact Instrument is turned on, the integral computer controls all instrument operations. The instrument is operated by the touch-screen and the barcode scanner only. The menus on the instrument touch-screen will guide you through instrument set up and operation.

Note: If you need additional information about a particular function, touch the Informa-

tion button to see a more complete description of the function.

1.1 Starting the MagNA Pure Compact Instrument

To start the MagNA Pure Compact Instrument, push the Power On button on the front of the instrument

Note: The Power On button is only used for start-

ing the instrument. To shut down the instrument, always use the Exit button on the computer touchscreen. (See below for location of this button.)

On start up, the program displays a START UP Screen while it loads the program and runs a start up self-test. The startup usually takes about oneminute.

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Handling the MagNA Pure Compact Software

Starting the MagNA Pure Compact Instrument

Table 1 below shows the systems examined during the self-test. If any test is not passed, the screen will display an error message. (For an overview of error messages, please see chapter C.)

Function Test

Instrument communication Check for correct communication between hardware and

software. Door sensor Function te st of sensor for locked front door. Magnetic sensor ON/OFF status must correspond to its position Home sensor Function test of sensor for robotic arm in home position. Waste tank sensor Check for presence of waste tank. Housing fan sensor Check for presence of housing fan.

Table 1: Overview of self-test

Note: If the self-test is not passed and the remedy as described in the section about errors

and troubleshooting does not help, please contact your local Roche representative.

Note: Besides the start up self-test, the instrument

will automatically perform a self-test after a certain period of instrument inactivity. You must confirm execution of this self-test on a message window.

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Handling the MagNA Pure Compact Software

Overview on Main Menu Screen

1.2 Overview of Main Menu Screen

After the self-test is complete, the MAIN MENU screen appears (figure 1). From this menu, you can easily access all the software submenus by touching the appropriate buttons.

Figure 1: Parts of the Main Menu Screen

1. Title of current menu/submenu

The left portion of the title bar lists the name of the menu or submenu currently displayed on the screen. Table 4 on page 41 shows an overview over menu and submenu structures.

2. Global Action Buttons

Touching one of the global action buttons will activate/execute the corresponding function. Table 2 at the end of this section gives an overview of the function buttons.

Note: If a function button appears in the background (i.e., is displayed in the background

color), it cannot be activated at this time.

3. Display field for error codes/information

A short error code is displayed here, if an error occurs. For an overview about instrument errors, please see chapter 4.2 Instrument Error Codes. An information window with a long information message pops up, if the appropriate global action button is activated.

4. Button for Instrument Shutdown

Solely shut down the instrument by touching this button.

5. Buttons for Submenus

You can access any submenu by touching one of the submenu buttons on the MAIN MENU screen. Table 4 at the end of this section describes the functions of the main menu and submenus. An overview of the maintenance submenu is given in chapter C, sections 1 and 2.

6. Status Indicator

The right portion of the Title Bar shows the current status of the instrument. For a list of possible statuses, see table 3 at the end of this section.

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Handling the MagNA Pure Compact Software

Overview on Main Menu Screen

Symbol Name Function

Keyboard Brings up a virtual keyboard. Only active when a text box that allows typed entries is high-

lighted. Regular set of symbols (mostly lower case) for virtual

keyboard (shift off):

Alternate set of symbols (mostly upper case) for virtual keyboard (shift on):

Print Prints current screen information, if a printer is connected locally.

Save Saves current screen information to the folder defined in the Setup submenu.

Home Returns to main screen. Inactive during processes that cannot be interrupted (e.g.: purifi-

cation runs)

Information Errors, warnings and additional informations are

displayed in the display for error codes/information.

To obtain more detailed information about the current software function or about the error history, select the information button; a pop-up window will open.

According to the type of message displayed, the Information button changes its color: Red Error Urgent information, act immediately.

Yellow Warning Information needs attention soon. Green Information Supplementary information, instrument is running OK.

Exit Exits the software program and switches the instrument

off. When you touch this button, a dialog box will appear to ask you to confirm the Shut Down command,

Table 2: Global action buttons

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Overview on Main Menu Screen

State Description, instrument action

Ready Self-tests OK, instrument is ready for operation, maintenance,

or service functions.

Error Instrument is shut down by fatal error or awaiting user intervention

after error

Running Protocol is beeing processed Run completed Run is completed, result screen is displayed. Leaky If the last leakage test has not been successful (state remains until

next O-ring change or next successful leakage test). Performing a purification run is not possible.

Table 3: Overview of Instrument Statuses

Submenu Function Described in Detailed Actions

Run Performing a purification run Chapter B Perform the sequence of steps on

the Sample Ordering Screens:

䉴 Operator Authorization 䉴 Sample Ordering 1 䉴 Sample Ordering 2 䉴 Sample Ordering 3 䉴 Sample Ordering 4 [available with IC] 䉴 Sample Ordering 5 䉴 Confirmation

Setup Setting basic information Chapter A Setting:

䉴 Time and Date 䉴 Operator administration 䉴 Laboratory name 䉴 Folder where results are saved 䉴 Sample material

Documentation Organizing

documentation

Maintenance Performing instrument

maintenance

Chapter B Documentation via:

䉴 Printouts 䉴 Saved result files

Chapter C Maintaining:

䉴 Leakage Test 䉴 Counter and Reminder 䉴 Error Log 䉴 O-ring Exchange 䉴 Liquid Waste Discard 䉴 UV Decon tamination

Service Performing specialized service

functions

Table 4: Overview of menu and submenu structure

How to Operate the MagNA Pure Compact Instrument

Not described in this Operator’s Manual.

Used by Roche service operators only

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General Workflow for Preparation of a Purification Run

1.3 Flow Diagram for Preparation of a Purification Run:

Workflow

Scan cartridge barcode

and insert cartridge

Selecting purification

protocol

Insert tip trays

Insert sample

[Insert tubes for internal control]

Insert elution tubes

Run the purification

protocol

Use elution tubes for

downstream application

Liquid waste handling

Remove disposables

Clean

Instrument ready

for next isolation

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2. Performing a Purification Run

Do not use the equipment in a manner not specified by the manufacturer (see pages 11-

12). Otherwise, the protection provided by the equipment might be impaired. For kit specific details regarding the handling of Reagent Cartridges, please see the

corresponding pack insert of the kit.

Warnings and Precautions when handling the Reagent Cartridges:

䉴 Wear pr otective disposable gloves, laboratory coats and eye protection when handling

samples and kit reagents, and follow usual safety precautions during handling. Avoid contact of the reagents from the kit with skin, eyes, or mucous membranes. If contact does occur, immediately wash with large amounts of water. Burns can occur if left untreated. If reagents are spilled, dilute with water before wiping dry.

䉴 Handle each Reagent Cartridge prior to use as follows:

䊉 Always adapt the Reagent Cartridge to room temperature (30 min). If you use the

reagents at temperatures outside the recommended range, the kit may not work well.

䊉 Check the cartridge sealing foil for any possible damage and the cartridge for

correct filling. Do not use a cartridge that does not appear as specified.

䊉 Always wear gloves when handling the MagNA Pure Compact reagent cartridge. 䊉 Hold the cartridge at the barcode imprinted area and the opposite side only. 䊉 Avoid touching the sealing foil covering the cartridge wells. 䊉 Avoid touching the two single open wells and do not use them as handles. 䊉 Mix the content of the cartridge wells by turning the whole cartridge upside down

several times.

䊉 Avoid any foam formation. 䊉 Let the fluid within the cartr idge wells settle again completely. If fluid or magnetic

glass particles remain under the sealing foil, knock the cartridge bottom gently on a flat lab bench surface. Note: Small drops may remain at the sealing foil (up to 30 µl).

䉴 Wash hands thoroughly after handling samples and test reagents. 䉴 Do not eat, drink, or smoke in the laboratory work area and do not pipet by mouth. 䉴 Some buffers c on tain th e hazardous compounds guanidine thiocyanate and guanidine

hydrochloride. Do not allow reagents containing guanidine thiocyanate to contact sodium hypochlorite (bleach) solution or acids. These mixtures produce a highly toxic gas.

䉴 All mammalian (especially human) material and all resulting waste is potentially

infectious. Thoroughly clean and disinfect all work surfaces with disinfectants recommended by the local authorities.

䉴 Dispose of unused reagents and waste in accordance with country, federal, state, and

local regulations.

䉴 Material Safety Data Sheets (MSDS) are available upon request from the local Roche

office.

䉴 Use sterile, disposable, nuclease-free pipette tips to avoid microbial and nuclease con-

tamination.

䉴 Do not use sharp or pointed objects near the reagent cartridge in order to prevent

damage of the sealing foil and loss of reagent.

䉴 Do not use a kit after its expiration date.

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Warnings and Precautions when handling the Tip Trays:

䉴 Check that piercing tool and reaction tips are placed correctly in the Tip Tr ays before

use.

䉴 Handle Tip Trays with care to prevent tips or piercing tool from falling out of the tray.

Should this happen, discard the respective tip tray and tips. Use the Tip Tr ay Kit to replace missing Tip Trays.

Note: To ensure that you have entered all essential information before starting the purifi-

cation run, the software screens will guide you through the steps for programming a purification run. At each screen, you must enter values in all para meter fields that are marked with a "*“ and press all confirmation buttons that are marked with a "?“ before you can go to the next screen. All fields that are not marked with a "*“ are for documentation only; you do not have to fill these in. Nevertheless, we recommend that you enter values in these fields, since this information may later help with troubleshooting.

Controls

Always run appropriate controls with the samples, especially if you want to perform quantification analyses of the eluted DNA samples (e.g., by LightCycler® 2.0 System PCR assays). In order to control the complete process starting from sample preparation to quantification analysis, perform the following controls:

䉴 Positiv e Control, by using a sample material positive for your target. 䉴 Negative Control, by using a sample material negative for your target. 䉴 Internal Cont rol, by adding a defined amount of a control template (e.g., plasmid

DNA) to all samples to be purified or by analyzing an endogenous nucleic acid sequence present in all your samples.

For the MagNA Pure Compact Nucleic Acid Isolation Kit and MagNA Pure Compact Nucleic Acid Isolation Kit - Large Volume:

The Internal Control (IC) is added prior to the purification step, then co-purified, and amplified with your target of interest from the specimen in the same PCR reaction. The IC concept is especially useful for enzyme-based amplification processes such as PCR, because inhibitors present in th e puri fied sample materi al mig ht reduce eff iciency of the PCR process. In addition, the Interna l Control is used to compensate for possible losses of your target during purification.

For LightCycler® 2.0 System quantification assays use a synthetic double-stranded DNA molecule with primer-binding sites identical to those of your target sequence, but having a unique probe-binding region that differentiates the IC from the target-specific amplicon. Discriminate the signals derived from your target and the IC by performing a dualcolor HybProbe assay. For detailed information regarding the IC concept in combination with the LightCycler® 2.0 System, read LightCycler® Technical Note 12/2000 “Absolute Quantification with External Standards and an Internal Control” available at http:// www.lightcycler-online.com.

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For the MagNA Pure Compact RNA Isolation Kit:

The selection of an appropriate endogenous IC is of high importance when developing a quantitative R T-PCR assay. The IC is co-amplified with the target of int er est and serves as a control for several factors: differences in initial template concentrations between different samples, sample-to-sample variations in the PCR, presence of PCR inhibitors or the extent of any RNA degradation. The advantage of using an endogenous IC is that both internal control mRNA and target mRNA is extracted from cells or tissue and reverse transcribed together. Commonly used endogenous ICs include so-called housekeeping gene mRNAs. (Note that Roche Applied Science offers several LightCycler® Housekeeping Gene Sets for the detection of human housekeeping genes, incl. G6PDH, HPRT, ALAS, and should not vary with the experimental conditions or treatments to be compared.

␤2-microglobulin.) The level of expression of an appropriate endogenous IC

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Performing a Purification Run

Purification

2.1 Purification

Action Handling Software programming

Performing a Purification Run

Purification

Please select the Run button from the Main Menu Screen to get to the following screen.

The OPERATOR AUTHORIZATION Screen appears. While at this screen, do the following:

a. Either accept the User name that appears in the

Operator field or select a different name from the drop-down menu (accessed by touching the Down button beside the field).

b. Enter the password

c. Cancel leeds back to the Main Menu.

d. Confirm your choices by touching the Next

button (which will be active only if the Operator and Password fields are filled in and the password is correct).

Note: You cannot add new operator names

from this screen; these must be added from the SETUP Screen (as described in chapter A 3.4.3).

To change the password associated with a particular operator name, touch the Change Password button. A pop-up window will open to allow you to enter the new password.

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Purification

Action Handling Software programming

Performing a Purification Run

Purification

Open the front door of the MagNA Pure Compact Instrument and remove all the racks you will need for the run:

a. Cartridge Rack

Pull the handle towards you to lift the Processing Stage. Pull the stage towards the front of the instrument to move the pin on the front of the stage to the top (wide part) of the keyhole in the Cartridge Rack. Now you can remove the Cartridge Rack.

b. Tube Racks

Remove the Tube Rack (which also holds the Elution Tube Rack) and place it on the laboratory bench, so you can easily insert the samples and (if appropriate) the internal controls according to the instructions that will appear on the touch-screen.

SAMPLE ORDERING SCREEN 1 appears. While at this screen, do either of the following:

䉴 Use the barcode scanner to scan the barcode of

the first prefilled Reagent Cartridge.

Note: In case you experience difficulties in scan-

ning the barcode:

• try to scan holding the barcode scanner in different angles

• wipe the barcode surface carefully before scanning

Result:

䉴 The instrument will display the name of the

appropriate purification kit.

䉴 On the overview diagram (upper left corner of

screen), cartridge position 1 (a) changes from the background color to green (indicating position 1is "active“).

䉴 The scanned barcode (b) appears in the first text field (Cartridge ID 1).

Alternatively, you may use the virtual keyboard to enter the barcode in the Cartridge ID field:

䉴 Touch the field to highlight it.

䉴 Type the Barcode number in the keyboard text

field.

䉴 Touch the Return key to transfer the number to

the Cartridge ID 1 field (on SAMPLE ORDERING SCREEN 1).

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Action Handling Software programming

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Purification

For best results, grab the flap that is on the opposite end of the cartridge from the two isolated wells. Then, with the two isolated wells pointing away from you, insert all the wells on the plastic cartridge into the holes in the cartridge rack. Use the guide slots on the rack to help position the cartridge.

Note: Make sure the cartridge fits all the way into the rack. Do not simply lay the cartridge on top of the

rack, since, if it sticks up, it may move during the run and cause the instrument to malfunction.

If you are going to process more than one sample during the current purification run:

Repeat the above cartridge identification and placement steps 4-5 for each prefilled cartridge until all (up to 8) cartridges are recorded on screen and inserted in the cartridge rack.

Result: On the overview diagram, the last added cartridge position will be green (a), and the previously added positions will be dark blue (b). The name of the appropriate purification kit will also be displayed (c).

Note: It is not possible to enter barcodes of the same

type (catalogue number). Barcodes from identical or expired cartridges are rejected.

When all cartridges have been programmed and inserted into the cartridge rack, do the following:

䉴 Reinsert the Cartridge Rack into the MagNA Pure

Compact Instrument. To reinsert the Cartridge Rack, fit the pin on the stage into the wide part of the keyhole on the rack, then push the rack back, which will also immobilize the pin in the narrow part of the keyhole. Now you can lower the stage by moving the handle away from you.

䉴 On SAMPLE ORDERING SCREEN 1, touch the

Cartridge Insertion confirmation button (a). After you touch the confirmation button, the symbol on the button changes from "?" to a checkmark.

䉴 The Next button (b) will now be active.

Touch this button to confirm the information on this screen and go to the next programming screen.

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Action Handling Software programming

Performing a Purification Run

Purification

SAMPLE ORDERING SCREEN 2 appears. While at this screen, do the following:

䉴 In the Protocol field, either accept the protocol (from the last run) that appears in the field or select another puri-

fication protocol from the adjacent pull-down menu. (Touch the Down arrow to the right of the field to access this menu.)

䉴 In the Sample Volume field, select a value from the adjacent pull-down menu.

䉴 In the Sampe Material field, select your sample

material from the adjacent pull-down menu.

䉴 In the Elution Volume field, select a volume from

the adjacent pull-down menu.

Note: For an overview about the possible

combinations of different sample and elution volumes, please refer to the respective pack insert of the purification kit. Combining of non recommended volumes may leed to suboptimal results (e.g. processing performance, yield, etc.)

䉴 (optional) If you are using an internal control,

select a control volume from the pull-down menu adjacent to the Internal Control Volume field: You can choose between 5, 10, or 20 µl. Default setting is None. Note, that some purification protocols do not allow an optional internal control.

.䉴 Insert the appropriate number of Tip Trays (one

per purification) in the instrument Tip Rack.

䉴 On SAMPLE ORDERING SCREEN 2, touch the

"Tip Trays inserted" confirmation button (1).

Result:

䉴 After you touch the "Tip Trays inserted" confirma-

tion button, the symbol on the button changes from "?“ to a checkmark (2). Also, the reagent layout diagram shows the tip trays inserted (in dark blue).

䉴 The Next button will now be active. Touch

this button to confirm the information on this screen and go to the next programming screen.

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Purification

Action Handling Software programming

Do one of the following:

Performing a Purification Run

Purification

SAMPLE ORDERING SCREEN 3 appears. While at this screen, do the following:

䉴 Pipet the correct type and amount of sample

material (as chosen on Sample Ordering Screen

2) into a sample tube (tube without barcode label,

from the reagent kit).

䉴 Identify the tube by attaching your own barcode

label or writing a number on the tube with a permanent marker.

䉴 Put the filled sample tube in position 1 on row 1

of the Tube Rack.

Note: It is recommended to use the

appropriate row in the tube rack for original sample tubes, if suitable for these tubes (e.g. max. 15 ml Falcon tubes).

䉴 On SAMPLE ORDERING SCREEN 3, touch Sample ID field 1. In that field, enter the ID of Sample 1 (i.e., the one

you just put in the rack) by either scanning the (self-attached) barcode or using the virtual keyboard to type the ID number. (Touch the Keyboard button to access the keyboard.)

䉴 (optional) In the Comment field, you may enter

additional information about Sample 1. (Touch the field to highlight it, then use the virtual keyboard.)

䉴 Repeat the above sample placement and

identification steps for each sample to be purified (e.g., for Sample position 2, 3, …, 8).

Result: As you fill in the "Sample-ID" field for each sample, the corresponding position in the reagent layout will change from green (active) to dark blue (installed in instrument).

If ... Then ...

You are not using internal controls (i.e., you selected a protocol with no internal control on SAMPLE ORDERING SCREEN 2) (Action 8 above)

You are using internal controls (i.e., you selected a protocol with internal control on SAMPLE ORDERING SCREEN 2)

䉴 Insert the tube rack into the MagNA Pure

Compact Instrument.

䉴 Touch the "Samples inserted" confirmation

button (a).

䉴 The Next button (b) will now be active. Touch

this button to confirm the information on this screen and go to the next programming screen (SAMPLE ORDERING SCREEN 5).

䉴 Go to Action 11 below.

䉴 Touch the "Sample inserted" confirmation

button (a).

䉴 The Next button (b) will now be active. Touch

this button to confirm the information on this screen and go to the next programming screen (SAMPLE ORDERING SCREEN 4).

䉴 Go to Action 10 below.

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Action Handling Software programming

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Purification

SAMPLE ORDERING SCREEN 4 appears.

Note: This screen only appears and accepts informa-

tion about Internal Control Tubes if you selected a protocol with internal controls on SAMPLE ORDERING SCREEN 2. (See Action 8 above). The program will skip this screen if you selected a protocol with no internal control.

Note: Pipette the lysed sample into the

Internal Control Tube before you place the tube in the cartridge. It is essential for this action to have an Internal Control Tube inserted!

䉴 Pipet the proper amount of internal control (as

specified on Sample Ordering Screen 2) into one of the Internal Control Tubes (not provided in kit; for purchase information, see chapter C).

䉴 Identify the tube by attaching your own barcode label or writing an ID number on the tube with a permanent

marker.

䉴 Put the filled control tube in position 1 on row 2 of the Tube Rack.

䉴 On SAMPLE ORDERING SCREEN 4, touch IC Sample ID field 1. In that field, enter the ID of Control 1

(i.e., the one you just put in the rack) by either scanning the (self-attached) barcode or using the virtual keyboard to type the ID number. (Touch the Keyboard button to access the keyboard.)

䉴 Repeat the above control placement and identification steps for each control used

(e.g., for Control position 2, 3, …, 8).

Result: As you fill in the "Internal Control ID" field for each control, the corresponding position in the reagent layout will change from green (active) to dark blue (installed in instrument).

䉴 Insert the Tube Rack with sample and internal controls into the MagNA Pure Compact Instrument.

䉴 Touch the "IC Tubes inserted" confirmation button.

䉴 The Next button will now be active. Touch this button to confirm the information on this screen and go to

the next programming screen.

SAMPLE ORDERING SCREEN 5 appears. While at this screen, do the following:

䉴 Put the appropriate number of Elution Tubes

(supplied in the purification kit, with barcode labels) into the Elution Tube Rack.

Note: Elution Tubes will contain the final purified

nucleic acid after it is eluted from the magnetic beads with elution buffer.

䉴 Either scan the barcode on each elution tube into

one Elution Tube ID field on SAMPLE ORDERING SCREEN 5 or type the tube ID into the field manually with the virtual keyboard.

For convenience you may insert all the tubes in the rack, then scan all their barcodes into the ORDERING screen at the same time (see picture). Alternatively, you may scan the barcode from each tube first, then insert it into the rack.

Result: As you fill the Elution tube ID field for each elution tube, the corresponding position in the reagent layout will change from green (active) to dark blue (installed in instrument).

䉴 Insert the filled Elution Tube Rack into the MagNA Pure Compact Instrument.

䉴 Touch the "Elution tubes inserted" confirmation button.

䉴 The Next button will now be active. Touch this button to confirm the information on this screen and go to

the next programming screen.

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Action Handling Software programming

Performing a Purification Run

The CONFIRMATION Screen appears. While at this screen, do the following:

䉴 Check the information display and:

- if the information is correct, confirm it by

touching the "Confirm Data" button, or

- if the information is not correct, touch the

Previous button as many times as necessary to go back to one of the earlier screens and change the erroneous information. Once the information is correct, touch the Next button

(repeatedly) to return to the CONFIRMATION screen, then touch the "Confirm Data" button.

䉴 Make sure the Drop Catcher is present on the

Preparation Stage, then touch the "Drop Catcher present" confirmation button.

䉴 Now the Start button will be active. Start the purification by touching this button.

The HEATING Screen will appear displaying the time needed for heating of the heating units.

When heating is completed, the PROCESS Screen will appear and remain throughout the entire purification run.

䉴 As the run progresses, this screen will display the

actual step being performed and the time remaining.

Note: If you need to interrupt the run before it is

complete, you can execute an emergency stop by touching the Cancel button. (Before the instrument actually stops the run, you will need to confirm the request twice by replying to dialog boxes that appear.)

䉴The instrument will sound an alarm when the run is

finished. (See Chapter A for information on setting this alarm.).

Purification

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Liquid Waste Discard

Action Handling Software programming

Performing a Purification Run

Liquid Waste Discard

After the purification run has ended, the RESULT screen appears.

䉴 The RESULT screen shows the result of the

isolation process for each channel:

- The result will be PASS if the isolation run was completed without any warning or error.

- The result will be FAIL if any interruption of the process or error occurred during the run. For each FAIL result, the result screen will show a brief error or warning messages (in the scrollable Result list or the Information text box) to help you decide whether the error or warning can be ignored.

Note: To investigate a potential error cause either

touch the Information button or use the Errorlog function from the Maintenance menu.

䉴 To set up for the next run, you must empty liquid waste from the Drip Tray, then touch the Liquid Waste

confirmation button on the RESULT screen.

Note: See chapter C for details on discarding liquid waste.

You can print and/or save the result by touching the appropriate function buttons (icons) at the bottom of the RESULT Screen.

Note: If you touch the Save button, a pop-up window

will open to allow you to specify the export format (plain text or XML) of the Result file. The export file is saved to the Save Folder defined under basic software settings (see Chapter A, Software setup for details). The file name is equal to the Run ID.

Take out the Elution Rack with the Elution Tubes for further use.

Close the Elution Tubes with the screw caps provided.

Note: The tubes can be screwed down with one

hand, as they are secured against turning by a mechanical anti-twist device.

MagNA Pure Compact Operator’s Manual - Version 1.3

Perform Liquid Waste Discard. Either discard all disposables containing liquid waste according to the relevant country specific regulations. Or use the automated function, which is accessible

a. via the Liquid Waste Discard button displayed on the RESULT screen

b. via the Maintenance Menue as described on the following pages in chapter B. 2.2

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Liquid Waste Discard

2.2 Liquid Waste Discard

Remove, empty and clean waste tank after each liquid waste discard.

Action Handling Software programming

Use the in-built liquid waste discard function of the MagNA Pure Compact Instrument to collect the reagents of one purification into the Waste Tank. Thereafter, you can discard the liquid waste following relevant country-specific saftey rules. The instrument will prompt the operator to empty the Waste Tank after every purification run.

䉴 On the Main Menu Screen touch the Mainte-

nance button. The Maintenance screen appears.

䉴 Touch the Liquid Waste Discard button.

Result: The Waste Discard Confirmation screen appears.

Performing a Purification Run

Liquid Waste Discard

䉴 Before performing the test, do the following in

the instrument:

- First, remove the Sample and Elution Tube Racks.

- Make sure the Tip Trays are still inserted.

- Make sure the Waste Tank is empty (but still in the instrument).

䉴 After you perform each of the actions in Step 2,

touch the appropriate button on the WASTE DISCARD CONFIRMATION Screen:

- Elution Rack removed confirmation button

- Tip Trays inserted confirmation button

- Waste Tank empty confirmation button

䉴 After you touch the three confirmation buttons,

the Start button will become active. Touch this button to make the instrument start transferrring liquid waste from the cartridges to the Waste Ta nk .

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Action Handling Software programming

After having touched the Start button,

䉴 the Nozzle Head will take up one tip from each

of the tip trays, aspirate the liquid from each individual well in the cartridge, and ejects it into the Waste Tank.

䉴 During the discard procedure, the screen will

display the time remaining in the procedure.

Note: You may interrupt the Liquid Waste Discard

procedure at any time by touching the Cancel button

䉴 After the Liquid Waste Discard procedure is com-

plete, the following message appears on the screen:

Note: The MagNA Pure Compact

Instrument does not automatically check the liquid level inside the waste tank. Always ensure that there is enough volume for uptake of liquid waste of one purification run. If the Waste Tank is too full, overflowing liquid will pour into the Drip Tray. However, if the overflow is too great, liquid waste will flow into into the instrument housing and even onto the lab bench. This will lead tp potential contamination and damage of the instrument.

Always empty the Waste Tank after each purification run, when asked by the instrument’s software to do so, or the instrument might be severely damaged! Treat the liquid waste as biohazardous material. Emtpy and clean waste tank as described in chapter C 3.1 Cleaning. If the Waste Tank should overflow, it is essential to clean the instrument according to the local regulations.

䉴 Open the instrument's front door by moving the lever at the right door side to the left.

䉴 Remove the Waste Tank and empty.

䉴 After confirmation the Close button appears.

䉴 Touch the Close button to return to the MAIN MENU or MAINTENANCE Screen.

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Internal Control

3. Use of Internal Controls

3.1 Function of Internal Control

If you are going to perform PCR on the purified nucleic acid and want to have an Internal Control (IC) for that PCR, we recommend that you add the IC to the sample before you purify it on the MagNA Pure Compact Instrument. Adding the IC at this stage allo ws you not only to estimate the efficiency of the PCR, but also the efficiency of the purification.

Note: For your convenience, many of the LightCycler® reagent kits already contain such

an IC. (See the pack inserts of these reagent kits for details).

3.2 How to program the instrument for an internal control

The IC may be added to the run of the MagNA Pure Compact Instrument in either of two ways:

Add the internal control directly to the sample:

When you program a run with an IC in the sample, do the following: On SAMPLE ORDERIN G Screen 2, choose a protocol „without IC“ in the Protocol field and specify „none“ in the Internal Control Volume field. In the Comment field, note that IC was added directly to the sample.

Note: Do not use this method if the IC is naked DNA ( e.g. plasmid) or RNA,

because the control may be degraded by nucleases present in the sample. Add the IC to one of the assigned IC positions in the Sample Tube Rack. Pipet the

IC (5, 10 or 20 µl) into a separate tube. (Use only the tubes specified in chapter C, since only they meet the instrument specifications.) Place the control tube in the IC row (row 2) of the Sample Tube Rack.

When you program the run with separate ICs, do the following: On SAMPLE ORDERIN G Screen 2, choose the protocol „with IC“ in the Protocol field and specify the correct volume of IC in the Internal Control Volume field. The instrument will automatically include the IC tubes in the purification process.

Note: The IC will be directly mixed with the Lyis Buffer at the beginning of the run

and will thus be protected from nucleases. Therefore, choose this method if your control is naked DNA or RNA.

As soon as one of the samples within a purification run is using IC, an IC tube has to be inserted in all channels that contain sample material (as indicated on the schematic on the screen).

Note: If you program a run with an IC, but do not place any tubes in the IC positions of

the Sample Tube Rack, the instrument will pipet Lysis Buffer through the empty IC tube postion directly onto the instrument stage. This spilled liquid may harm the operator as well as the instrument. If this happens, you should immediately clean the instrument (as described in chapter C) to prevent corrosion of the instrument stage. Always use gloves when you touch the instrument or reagents, and observe the instructions on the Material Safety Data Sheet that accompanies the reagents.

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Data Transfer from or to the MagNA Pure Compact Instrument

Data Transfer to other Instruments

4. Data Transfer to or from the MagNA Pure Compact Instrument

The data from the result screen can be saved to a disk. In future applications with the LightCycler System and COBAS TaqMan 48 Analyzer these data files can be transferred to the respective instruments.

4.1 Data Transfer to other Instruments

䉴 Data transfer to the LightCycler® System

You may create a text file of MagNA Pure Compact Run information and results that may be used on the LightCycler® System.

Note: Details on the creation of this file are contained in a separate document.

䉴 Data transfer to COBAS TaqMan 48 Analyzer

You may create a text file of the purification run of the MagNA Pure Compact Instrument containing information and results that may be used on the COBAS TaqMan 48 Analyzer.

Note: Details on the creation of this file are contained in a separate document.

4.2 Upload of New or Updated Purification Protocols

As new or updated purification protocols are created, they may be added to the MagNA Pure Compact Instrument via external data carrier disks (e.g. software update disk) during program start up. Additional protocols will be available for download from http://www. magnapure.com. Follow the download instructions on this web site. Always save the downloaded protocol files onto a newly formatted floppy disk.

Note:

䉴 Update disks will automatically be checked for viruses by the instrument software. 䉴 Each protocol file contains information on which reagent kits may be used with the

protocol. The instrument will use this information [kit name and kit number (included as a barcode on kit cartridges)] to verify and decode the scanned cartridge barcodes when you scan them into the SAMPLE ORDERING Screens. (See section B.2 for details.)

Workflow:

1. MagNA Pure Compact Instrument must be shut down.

2. Insert update disk.

3. Switch on instrument.

4. Software is automatically updated.

5. After Main Screen is displayed, remove update disk.

6. Update complete.

7. The instrument is ready for use.

How to Operate the MagNA Pure Compact Instrument

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MagNA Pure Compact Operator’s Manual - Version 1.3

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Maintenance and Trouble Shooting

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MagNA Pure Compact Operator’s Manual - Version 1.3

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User Maintenance

Leakage Test

Maintenance and Trouble Shooting

1. User Maintenance

User Mainte nance c onsists besid e r egular cleaning mostly of a regular check of the Nozzle Head function. Other regular activities for the operator are mentioned throughout this manual. In order to check the proper function the following routine checks are recommended and explained in the course of this chapter.

Leakage Test: every 50 purification runs or every second month or if the

Nozzle Head seems to show leakage

O-ring maintenance: Greasing of O-rings: every 20 purification runs or once a week

Exchange of O-rings: If the Leakage Test indicates

It is recommended to start a ring-binder with the new instrument, where all operator maintenance, cleaning and service engineer maintenance is documented. There should be documented also regular checks of the system performance. If you need assistance in creating such ring-binder, please contact your local Roche representative.

As well it is advisable to document there or in the MagNA Pure Software documentation all operators and used reagent kit lot no.s in order to be able to perform an optimal trouble shooting, if needed.

1.1 Leakage Test

Purpose

The Leakage Test will detect any leakage of air into the reaction tips, which might eventually lead to loss of liquid. If there is a leak, the most probable cause is deteriorated or damaged O-rings (on the Nozzle Head).

Use

We recommend that you perform a Leakage Test after two months or after 50 purifications. You should also perform a Leakage Test any time you suspect that the pipet tips are leaking.

Note: Although wear and tear-on the O-rings is related to the number of isolations per-

formed, it is also influenced by maintenance (e.g. if the O-rings are not greased often enough) and environmental conditions (e.g. light, chemicals). Because of this, we recommend that you regularly test for leakage, even if the instrument is not used regularly.

Maintenance and Trouble Shooting

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User Maintenance

Leakage Test

After each Leakage Test, do one of the following:

If the Leakage Test shows that the O-rings...

are leaking and need to be changed 䉴 change the O-rings (as described in Section

are O.K. do nothing now, but repeat the test after another two

Performing of the Leakage Test

Disposables needed:

Cat. No. Product Content

03 561 429 001 MagNA Pure LC O-Ring Maintenance Kit O-rings (12 x 8), Grease (1) 03 753 166 001 MagNA Pure Compact Tip Tray Kit 10 Tip Trays Sarstedt Tubes as recommended in chapter C.5.1 Related Pro-

ducts

䉴 Launch the MagNA Pure Compact soft-

ware.

Then ...

C.1.2.2).

䉴 perform the Leakage Test again, to make sure the

new O-rings are working correctly.

months or 50 purification runs.

䉴 On the MAIN MENU Screen that

appears, touch the Maintenance button.

䉴 On the MAINTENANCE Screen that

appears, touch the Leakage Test button.

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䉴 Put 8 new Tip Tr ays (from the Roche Tip

Tray Kit) into the Tip Tray Rack.

䉴 Pipet 1 ml water into each of 8 Sarste dt

tubes, then insert the tubes into row 1 (Sample Tube row) of the Tube Rack.

䉴 Place 8 empty Sarstedt tubes into the Elu-

tion Tube Rack.

䉴 After doing each of the above steps, touch

the correct confirmation button on the touch-screen:

• "Filled tubes in sample position" confirmation button

• "Empty tubes in elution position" confirmation button

• "Tip trays inserted" confirmation button

䉴 As you touch each confirmation button,

the "?" symbol on the button changes to a checkmark.

User Maintenance

Leakage Test

䉴 After you touch the three buttons, the

Start Test button will become active. Touch it to start the test.

As the instrument performs the Leakage Test described below, the screen will display the time remaining.

Note: To cancel the test at any time, touch

the Cancel button.

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User Maintenance

Leakage Test

Instrument actions during the Leakage Test:

At the beginning of the test, the robotic arm picks up the tips and moves to the

Sample/Internal Control Tube Rack. The arm aspirates 1 ml of water plus an additional 100 µl of air from the sample tubes.

The stage moves the empty Elution Tubes under the Nozzle Head.

The Nozzle Head moves to a position directly in front of the Magnetic Plate and

raises the nozzles until the water meniscuses in the Reaction Tips are even with the upper rim of the Magnetic Plate.

The Nozzle Head holds this position for 10 min. While the Nozzle Head is holding

position, open the instrument door, so you can more easily observe the Nozzle Head.

Watch the water level within the Reaction T ips. If the water level remains the same

in all tips, none of the tips is leaking. If you observe different water levels in different tips or drops of liquid falling into the sample tubes, one or more nozzles is leaking. As a final check, visually inspect the empty Elution Tubes for liquid, as well as the Nozzle Head. If there has been leakage, change the O-rings as described in Section C.1.2.2.

Note: Some leakage can be tolerated. If, after 10 minutes, the difference in water

levels between tips is less than 4 mm, you do not need to change the O-rings. After 10 min, close the instrument door.

Result: The instrument will eject the water back into the Sample Tubes and the Reaction Tips are placed back in the Tip Tray. After the Leakage Test is complete, the Leakage Test Result screen is displayed.

䉴Touch the appropriate button to

document the test results.

䉴T ouch the Close button to return

to the MAINTENANCE Screen.

Note: As soon as Leakage has been confirmed, the State indicator will permanently show

LEAKY until the O-rings are changed and No Leakage has been confirmed.

MagNA Pure Compact Operator’s Manual - Version 1.3

Roche MagNA Pure Compact Instrument Operator's Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

Table of Contents

Table of Contents

Intended Use of the Instrument

Contact Addresses

Prologue

Revision History

Marks of Conformity

How to Use this Manual

Symbols used in this Manual

General Overview

1 Specifications of the Instrument

1.1 General Information

1.2 Operating Environment

1.3 Operating Parameters

2 Installation of the Instrument

2.1 Shipping

2.2 Unpacking

2.3 Additional Items Required for Operation and Maintenance

2.3.1 Operating Reagents

2.3.2 Maintenance Items

2.4 Setup

2.4.1 Selecting a Location

2.4.2 Easy Teaching Procedure

2.4.3 Software Setup

3 Description of the Instrument

3.1 General Description

3.2 Function Principle

3.3 Description of the Instrument

3.3.1 Front View of the Instrument

3.3.2 Detailed view

3.3.3 Back View of the Instrument Description of Instrument Backmber Instrument Part Description

3.3.4 Sides of the Instrument

3.3.5 MagNA Pure Compact Accessories

3.3.6 Position and Meaning of Warning Labels

How to Operate the MagNA Pure Compact Instrument

1. Handling the MagNA Pure Compact Software

1.1 Starting the MagNA Pure Compact Instrument

1.2 Overview of Main Menu Screen

1.3 Flow Diagram for Preparation of a Purification Run:

2. Performing a Purification Run

3. Use of Internal Controls

3.1 Function of Internal Control

3.2 How to program the instrument for an internal control

4. Data Transfer to or from the MagNA Pure Compact Instrument

4.1 Data Transfer to other Instruments

4.2 Upload of New or Updated Purification Protocols

Maintenance and Trouble Shooting

1. User Maintenance

1.1 Leakage Test