Roche MagNA Pure 96 Setup guide

MagNA Pure 96 System
Customer Training Guide, Version 1.0
Software Version 2.0 December 2010

Table of Contents
3
Prologue 5
I Revision History ............................................................................................................................................... 5
II Contact Addresses ........................................................................................................................................ 5
III Trademarks ........................................................................................................................................................ 6
IV Intended Use ..................................................................................................................................................... 6
V Conventions Used in this Guide ............................................................................................................. 6
VI Warnings and Precautions ........................................................................................................................ 8
A Start-up 11
1 Starting the MagNA Pure 96 Instrument ....................................................................................... 11
2 Starting the MagNA Pure 96 Software ........................................................................................... 12
3 Preparing the MagNA Pure System .................................................................................................. 13
3.1 System fluid ....................................................................................................................................................... 16
3.2 Waste containers ............................................................................................................................................. 20
B Main Applications 27
1 Setting up a Run for Purification of Genomic DNA from Whole Blood Samples .... 29
1.1 Preparing the Samples .................................................................................................................................. 29
1.2 Defining the Parameters in the Software ............................................................................................... 32
1.3 Loading the Stage ........................................................................................................................................... 34
2 Setting up a Run for Purification of Cellular RNA from Cultured Cells ......................... 43
2.1 Preparing the Samples .................................................................................................................................. 43
2.2 Defining the Parameters in the Software ............................................................................................... 44
2.3 Loading the Stage ........................................................................................................................................... 46
3 Performing a Run ......................................................................................................................................... 51
3.1 Starting a Run ................................................................................................................................................... 51
3.2 Monitoring the Run ........................................................................................................................................ 51
3.3 End of a Run ..................................................................................................................................................... 52
4 Unloading the Instrument ....................................................................................................................... 54
4.1 Handling Partially Used Reagent Sets ..................................................................................................... 56
4.2 Handling the Waste ........................................................................................................................................ 58
4.3 Cleaning .............................................................................................................................................................. 58
5 Performing a Volume Transfer ............................................................................................................. 59
5.1 Defining the Parameters in the Software ............................................................................................... 59
5.2 Loading the Stage ........................................................................................................................................... 61
C Shutting Down the System 67
D Appendix 69
1 Index ................................................................................................................................................................... 69

MagNA Pure 96 System, Customer Training Guide V1.0
Table of Contents
4

Prologue
Revision History
5
Prologue
I Revision History
© Copyright 2010, Roche Diagnostics GmbH. All rights reserved.
Information in this document is subject to change without notice. No part of this document may be re-
produced or transmitted in any form or by any means, electronic or mechanical, for any purpose, without
the express written permission of Roche Diagnostics GmbH.
Questions or comments regarding the contents of this guide can be directed to the address below or to
your Roche Diagnostics representative.
Roche Diagnostics GmbH
Roche Applied Science
Customer Support
Nonnenwald 2
82372 Penzberg, Germany
Every effort has been made to ensure that all the information contained in the MagNA Pure 96 Customer
Training Guide is correct at the time of printing.
However, Roche Diagnostics GmbH reserves the right to make any changes necessary without notice as
part of ongoing product development.
II Contact Addresses
Customer Training
Guide Version
Software Version Revision Date Changes
V1.0 V2.0 December 2010
Manufacturer Roche Diagnostics Ltd.
Forrenstrasse
CH-6343 Rotkreuz
Switzerland
Distribution Roche Diagnostics GmbH
Sandhofer Straße 116
D-68305 Mannheim
Germany
Distribution in USA Roche Diagnostics
9115 Hague Road
PO Box 50457
Indianapolis, IN 46250
USA

MagNA Pure 96 System, Customer Training Guide V1.0
Trademarks
6
III Trademarks
LIGHTCYCLER, LC, MAGNA PURE, COBAS, COBAS INTEGRA, AMPLICOR, HIGH PURE,
TRIPURE, GENOPURE and MAGNA LYSER are trademarks of Roche.
E-PLATE and ACEA BIOSCIENCES are registered trademarks of ACEA Biosciences, Inc. in the US.
ProbeLibrary and LNA are registered trademarks of Exiqon A/S, Vedbaek, Denmark.
Other brands or product names are trademarks of their respective holders.
IV Intended Use
The MagNA Pure 96 System is a robotic instrument for automated isolation of nucleic acids (DNA, total
RNA, total viral nucleic acids) from different kinds of biological research sample material (whole blood,
serum, culture cells, etc.) using the specifically designed MagNA Pure 96 Kits, for the purpose of life
science research only.
The MagNA Pure 96 System is intended for life science research only. It is not for use in diagnostic pro-
cedures.
The system was neither developed nor validated by the manufacturer for any kind of in vitro diagnostic
application.
Any use of the MagNA Pure 96 System as a front-end sample preparation system for in vitro diagnostic
test systems such as COBAS®AMPLICOR®Instrument tests is the sole responsibility of the operator. The
validation of the combination of MagNA Pure 96 System nucleic acid isolation and in vitro diagnostic
testing must be performed by the operator, following the relevant national regulations.
V Conventions Used in this Guide
Text Conventions
To present information that is consistent and easy to read, the following conventions are used in this
Customer Training Guide:
Numbered list Steps in a procedure that must be performed in the order listed.
Italic type Used for operating instructions for the MagNA Pure 96 Software. In addition,
important notes and information notes are shown in italic type.
Green italic type Refers to a different section in this Customer Training Guide, which should be
consulted.

Prologue
Conventions Used in this Guide
7
Abbreviations
The following abbreviations are used in this Customer Training Guide:
Symbols
In this Customer Training Guide symbols are used as visual signals:
Abbreviation Meaning
CUL Canada Underwriters Laboratories
DNA Deoxyribonucleic Acid
IC Internal Control
LED Light Emitting Diode
MGP Magnetic Glass Particles
MSDS Material Safety Data Sheets
PBS Phosphate Buffered Solution
PCR Polymerase Chain Reaction
RNA Ribonucleic Acid
UV Ultraviolet
WEEE Waste Electrical and Electronic Equipment
Symbol Heading Description
WARNING This symbol is used to indicate that non-compliance with in-
structions or procedures could lead to physical injury or even
death or could cause damage to the instrument.
HOT SURFACE This symbol is used to label potentially hot
instrument surfaces.
BIO HAZARD This symbol is used to indicate that certain precautions must be
taken when working with potentially infectious material.
DANGEROUS ELECTRICAL
VOLTAGE
This symbol is used to indicate the danger of personal injury
due to dangerous electrical voltage. Refers to an imminent dan-
ger that may result in death or serious personal injury.
ULTRAVIOLET LIGHT This symbol indicates that the MagNA Pure 96 Instrument con-
tains high-energy ultraviolet lamps which can cause serious
temporary eye and skin irritation. Never expose unprotected
eyes or skin to the UV light.
IMPORTANT NOTE Information critical to the success of the procedure or use of the
product.
INFORMATION NOTE Additional information about the current topic or procedure.
   Procedure continued on next page.
End of procedure.

MagNA Pure 96 System, Customer Training Guide V1.0
Warnings and Precautions
8
The following symbols appear on the instrument
VI 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 electric shock or injury if not operated
according to the procedures in this Customer Training Guide.
Failure to comply with the instructions in this Customer Training Guide will void the manufacturer’s
warranty and may expose the operator to danger.
Make sure you carefully read and understand the Roche Diagnostics safety statements contained in this
section. This information should be kept for future reference and made available to new employees. Al-
ways keep this Customer Training Guide available near the MagNA Pure 96 Instrument for use by all op-
erators.
Symbol Heading Description
MANUFACTURER OF
DEVICE
On the instrument type plate.
CE MARK The CE mark on the instrument type plate indicates conformity
with requirements of the directives relevant for this instrument.
cUL MARK On the instrument type plate.
HOT SURFACE On the front panel behind the load flap of the instrument.
KEEP HANDS CLEAR On the front panel behind the load flap of the instrument.
The process station moves in a vertical direction. This causes the
risk of crushing hands in this movable part.
BIO HAZARD On the front panel behind the load flap of the instrument.
DANGEROUS ELECTRICAL
VOLTAGE
On the back of the instrument near the power box.
ULTRAVIOLET LIGHT On the supporting frame behind the maintenance flap of the in-
strument.
WEEE Electrical and electronic equipment marked with this symbol is
covered by the European directive WEEE.
The symbol denotes that the equipment must not be disposed of
in the municipal waste system.

Prologue
Warnings and Precautions
9
Handling Precautions
General Precautions
The MagNA Pure 96 Instrument is designed to ensure safe operation. However, since biological research
sample material may be processed in the instrument, there is a possible risk of infection. Therefore, when
handling potentially infectious material, always follow standard safety procedures and bear in mind the
following steps to minimize the chance of contamination or infection.
The instrument should not be used to analyze infectious materials unless additional safety measures to
ensure safe sample handling (e.g., placing the instrument in a laboratory with the appropriate safety
level, or using a purification protocol which allows external sample lysis) are taken beforehand.
Always wear a laboratory coat, gloves and a mask when handling specimens and reagents.
Immediately disinfect spills with an appropriate disinfectant solution to avoid spreading contamina-
tion to laboratory personnel or equipment.
If a specimen or other biohazardous material spills on the instrument or any of the racks, clean the
area or rack with a 10% (v/v) bleach solution (0.5% sodium hypochlorite) and then with a 70% etha-
nol solution.
Do not let water or chemicals come into contact with any electrical components.
Water or chemicals may cause damage and will void your warranty.
Unplug the equipment if it will not be used for extended periods of time.
When using the equipment, follow generally accepted procedures for quality
control and method development.
Do not attempt to disassemble the equipment. Repairs must be performed by
Roche service personnel. The equipment contains no operator-serviceable
parts.
Do not modify any part of the equipment. Modification may cause fire or mal-
function, or may void the manufacturer’s warranty.
Do not change or modify the purification protocols provided in the
MagNA Pure 96 Software. This will lead to malfunction of the MagNA Pure 96
System.
Anti-virus software is not provided. It is therefore essential to take precautions to
ensure that any software loaded onto the system is free of viruses. It is recom-
mended to install only Roche software on the control unit.
Make sure the main switch is freely accessible.
Warning of electric shock. Keep all covers closed while the instrument is con-
nected to the main power supply.
Spraying liquid on electrical parts can cause a short circuit and result in fire.
Keep the covers closed while the instrument is connected to the main power and
do not use spray in the vicinity of the MagNA Pure 96 Instrument.
Warning of explosion from sparks. Keep all potentially inflammable or explosive
material (e.g., anesthetic gas) away from the instrument.
The incubator of the process station is hot while the instrument is in operation.
Do not touch the surface of the heating block. The block is hot enough (up to
+100°C) to cause immediate burning.
Do not insert hands or fingers into either of the holes provided for discarding
waste liquids (on the right of the stage). If the reagent-dispensing nozzle head
moves suddenly, it may strike and injure your hand or fingers.
The instrument contains high-energy ultraviolet lamps which can cause serious
temporary eye and skin irritation. Never expose unprotected eyes or skin to the
UV light.

MagNA Pure 96 System, Customer Training Guide V1.0
Warnings and Precautions
10
If you are handling infectious, potentially infectious or any other dangerous material on the
MagNA Pure 96 Instrument, you must follow your country-specific guidelines and national, federal,
state and local regulations. Material Safety Data Sheets (MSDS) are available on request from your lo-
cal Roche Diagnostics representative or at www.roche-applied-science.com when searching for the
specific catalog of the respective product.
Discard unused reagents and waste (solid and liquid) in accordance with national, federal, state and
local regulations.
If this Customer Training Guide deviates from your national guidelines in any way, always follow your
national guidelines. This may mean, for example, that you must use additional or alternative disinfec-
tants or cleaning methods.
After sample preparation is complete, remove and autoclave all disposables if you were working with
infectious sample material.
After cleaning the stage with bleach and water/ethanol, decontaminate the instrument using the built-
in UV lamps. For more information, see section "Operator Maintenance" of the "MagNA Pure 96
Operator’s Guide".
Bleach can be used for disinfection and removal of contaminating nucleic acids and nucleases at the
same time. For sole disinfection purposes, you may also use commercially available disinfection re-
agents (please contact the respective distributors in your country for more information). For removal of
contaminating nucleic acids and/or nucleases, decontaminating agents such as LTK-008 or DNAZap
may be used. Be aware that decontamination agents do not disinfect. Please follow the instructions of
the respective manufacturer (for more information on decontamination agents see section "Operator
Maintenance" of the "MagNA Pure 96 Operator’s Guide").
The MagNA Pure 96 Instrument is not a fully airtight device. There is an air flow under the instru-
ment platform. Although all air flow from the platform is filtered through the dust filters (see section
"Main Components" of the "MagNA Pure 96 Operator’s Guide" for more information), it cannot be
guaranteed that the platform atmosphere never leaves the instrument without prior filtration by the
filter.
Therefore the MagNA Pure 96 Instrument does not have the same functionality as a laminar flow
biological safety cabinet and should not be used for analysis of infectious sample material that can be
transmitted by air, unless additional safety measures ensure safe sample handling.
Electrical Safety
The MagNA Pure 96 Instrument is designed in accordance with Protection Class I
(IEC). The chassis/housing of the instrument is connected to a protection earth (PE)
by means of a cord. For protection against electric 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 encoun-
tered, a qualified electrician must replace it with a properly (PE) grounded recepta-
cle in accordance with the local electrical regulations. An extension must not be
used. Any break in the electrical ground path, whether inside or outside the instru-
ment, could create a hazardous condition. Under no circumstances should the op-
erator attempt to modify or deliberately override the safety features of this instru-
ment. If the power cord becomes cracked, frayed, broken, or otherwise damaged, it
must be replaced immediately with the equivalent part from Roche Diagnostics.

Start-up
Starting the MagNA Pure 96 Instrument
11
A
A
Start-up 0
Before preparing a run, start the instrument and the control unit.
1 Starting the MagNA Pure 96 Instrument
The main switch of the MagNA Pure 96 Instrument is located on the bottom right side of the instrument.
See chapter "System Description" in the "MagNA Pure 96 Customer Training Guide" for a detailed de-
scription of the instrument parts.
To start the MagNA Pure 96 Instrument
Open the load flap.
Ensure that
The internal or external system fluid container is not empty. If it is empty, see sections To replace the
internal system fluid container or To replace the external system fluid container to replace it.
The internal waste container is drained. If it needs to be drained, see sections To drain the internal
waste container.
Close the load flap.
Press the main switch. When the initialization procedure has finished successfully, the LED on the right
of the front panel glows green, indicating that the instrument is ready for run preparation.
The instrument needs about four minutes for initialization.


MagNA Pure 96 System, Customer Training Guide V1.0
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Starting the MagNA Pure 96 Software
A
A2 Starting the MagNA Pure 96 Software
To start and log on to the MagNA Pure 96 Software, follow the steps below.
If you have accidentally locked the Windows XP operating system, login to Windows XP as MP96User
with the password MPDev09. The MP96User is an additional account which is automatically activat-
ed during startup of the control unit.
Switch on the monitor and the control unit. The Windows XP operating system is started.
Wait until Windows XP has completely finished startup - at least two minutes.
Double-click the MagNA Pure 96 Software icon on the desktop.
The application provides a splash screen with information on the initialization status. After initialization
the main window with the Overview tab is displayed.
Click LogOn in the global action bar. The LogOn dialog box opens.
Enter your User ID and Password.
User ID:Admin
Initial Password:MagNAPure96
These values specify the admin user for the MagNA Pure 96 Software and the initial password. Af-
ter entering the initial password at the first time you login, you are prompted to change the admin
password. For more information on changing the password, see chapter "Software" in the
"MagNA Pure 96 Operator’s Guide".
It is recommended that you create another user with the local administrator role. Only a local ad-
ministrator can reset the password of another local administrator.
Define a standard user as described in the "MagNA Pure 96 Operator´s Guide" if not already done.
The following procedures are described after login of a standard user.
Click OK.TheLogOn dialog box closes and the MagNA Pure 96 Software main window with the
Overview tab is displayed.


Start-up
Preparing the MagNA Pure System
13
A
A
3 Preparing the MagNA Pure System
On the first startup of the instrument each day perform the following steps:
Prime the instrument at least once, see next section.
Confirm that the instrument was cleaned before switch-off, see section To confirm clean instrument.
Confirm Daily Maintenance, see section To confirm daily maintenance.
Check visually if there is enough system fluid available. If necessary, change the system fluid container,
see section System fluid.
Check visually if there is enough space in the waste container. If necessary, change the waste container,
see section Waste containers.
To prime the instrument
In the MagNA Pure 96 Software, select the Instrument tab.
In the Instrument tab, select the Maintenance & Service sub-tab.
In the tree view, select Daily Maintenance. The substructure below Daily Maintenance is expanded.
Select the check box in front of Prime.
In the global action bar click Start. The MagNA Pure 96 Instrument is primed. When the priming is fin-
ished successfully, the Prime entry in the tree view is marked with the symbol.


MagNA Pure 96 System, Customer Training Guide V1.0
14
Preparing the MagNA Pure System
A
ATo confirm clean instrument
Ensure that the instrument is cleaned properly, see section Cleaning and chapter "Maintenance and Care"
in the "MagNA Pure 96 Operator’s Guide".
In the MagNA Pure 96 Software, select the Instrument tab.
In the Instrument tab, select the Maintenance & Service sub-tab.
In the tree view, select Daily Maintenance. The substructure below Daily Maintenance is expanded.
Select the check box in front of Confirm Clean Instrument.
In the global action bar click Start.Confirm Clean Instrument in the tree view is marked with the
symbol.


Start-up
Preparing the MagNA Pure System
15
A
A
To confirm daily maintenance
In the MagNA Pure 96 Software, select the Instrument tab.
In the Instrument tab, select the Maintenance & Service sub-tab.
In the tree view, select Daily Maintenance. The substructure below Daily Maintenance is expanded.
Select the check box in front of Confirm Daily Maintenance.
In the global action bar click Start.TheConfirm Daily Maintenance and Daily Maintenance entries in the
tree view are marked with the symbol.


MagNA Pure 96 System, Customer Training Guide V1.0
16
Preparing the MagNA Pure System
A
A
System fluid
3.1 System fluid
The system fluid is needed to clean the needles after each pipetting step and is used as a wash buffer for
the isolation of DNA and viral nucleic acids. For more information on system fluid, see chapter "System
Description" in the "MagNA Pure 96 Operator’s Guide".
There is either an internal or an external container for the system fluid. The MagNA Pure 96 Instrument
checks if there is enough system fluid left for a purification run of 96 samples. If there is not enough, the
status of the system fluid is indicated as inadequate in the instrument status area of the Stage sub-tab in
the MagNA Pure 96 Software. In this case, replace the system fluid.
To replace the internal system fluid container
If an internal system fluid container is used, proceed as follows
Open the load flap.
Pull the empty system fluid container halfway out of its compartment.
Do not pull the container completely out of its compartment, to avoid pinching the tube.
Remove the screw cap from the new system fluid container.
  

Start-up
Preparing the MagNA Pure System
17
A
A
System fluid
Press the release knob on the aspiration port and extract the tube.
Place the tube in the holder in the top left corner of the compartment frame.
Remove the aspiration port from the empty container.
To prevent contamination of the aspiration port, transfer it immediately into the new system fluid
container.

MagNA Pure 96 System, Customer Training Guide V1.0
18
Preparing the MagNA Pure System
A
A
System fluid
Remove the empty system fluid container and place the new one halfway in its compartment.
Place the aspiration port in the new container.
Connect the tube to the aspiration port. When you hear a click the tube is fixed.
Insert the new system fluid container completely into its compartment.
In the MagNA Pure 96 Software switch to the Workplace tab and then to the Stage sub-tab.
In the instrument status area click Replace.TheReplace System Fluid dialog box opens.
Enter the barcode of the new system fluid container with the handheld barcode scanner. The barcode is
displayed in the Barcode field.
Click OK. The system fluid indicator in the instrument status area is displayed in green to show the ap-
propriate status.
Close the load flap.
Discard the empty system fluid container according to local regulations.


Start-up
Preparing the MagNA Pure System
19
A
A
System fluid
To replace the external system fluid container
If there is not enough system fluid available for a purification run of 96 samples the MagNA Pure 96
Software indicates the system fluid status as inappropriate in the instrument status area of the Stage sub-
tab. If you are using an external system fluid container proceed as follows:
Remove the screw cap from the new system fluid container.
Remove the aspiration port from the empty container and insert it into the new container.
To prevent contamination of the aspiration port, transfer it immediately into the new system fluid
container.
In the MagNA Pure 96 Software switch to the Workplace tab and then to the Stage tab.
In the instrument status area click Replace.TheReplace System Fluid dialog box opens.
Enter the barcode of the new system fluid container with the handheld barcode scanner. The barcode is
displayed in the Barcode field.
Click OK. The system fluid indicator in the instrument status area is displayed in green to show the ap-
propriate status.
Discard the old system fluid container according to local regulations.


MagNA Pure 96 System, Customer Training Guide V1.0
20
Preparing the MagNA Pure System
A
A
Waste containers
3.2 Waste containers
The waste container collects the liquid waste during a purification run. There is either an internal or an
external container for the liquid waste. The MagNA Pure 96 Instrument checks if there is enough capacity
left in the waste container for a purification run of 96 samples. If there is not, the capacity status of the
waste container is indicated as inadequate in the instrument status area of the Stage sub-tab in the
MagNA Pure 96 Software.
In this case, drain the waste container.
To drain the internal waste container
Open the load flap.
Pull the waste container out of its compartment.
Pull the internal waste container carefully out of its compartment, to avoid pinching the tube.
Press the release knob on the connector and carefully extract the tube so as not to spill any liquid waste
on the instrument.
If the release knob is too stiff, grease the gasket of the tube of the internal waste container using
high-vacuum grease.
  