Qiagen Rotor-Gene Q MDx CE User manual

Sample to Insight__
February 2022
Rotor-Gene®Q MDx CE User
Manual
9002022
, 9002032, 9002042
QIAGEN GmbH
QIAGEN Strasse 1, 40724 Hilden, GERMANY
R
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Contents
1Introduction .............................................................................................................8
1.1 About this user manual....................................................................................8
1.2 General information........................................................................................9
1.2.1 Technical assistance................................................................................9
1.2.2 Policy statement......................................................................................9
1.2.3 Version management ............................................................................10
1.3 Intended use of the Rotor-Gene Q MDx...........................................................10
1.3.1 Requirements for Rotor-Gene Q MDx ......................................................10
1.4 Materials required ........................................................................................11
1.5 Materials required but not provided................................................................11
2Safety Information ..................................................................................................12
2.1 Proper use ...................................................................................................13
2.2 Electrical safety ............................................................................................15
2.3 Biological safety...........................................................................................16
2.4 Chemical safety............................................................................................17
2.5 Waste disposal ............................................................................................18
2.6 Mechanical hazards .....................................................................................18
2.7 Maintenance safety ......................................................................................20
2.8 Symbols on the Rotor-Gene Q MDx ................................................................21
3General Description ...............................................................................................22
3.1 Rotor-Gene Q MDx principle .........................................................................22
3.1.1 Thermal performance ............................................................................22
3.1.2 Optical system .....................................................................................23
3.1.3 Available channels ...............................................................................24
3.2 External features of the Rotor-Gene Q MDx .....................................................25
3.2.1 Air vents on the lid................................................................................25
3.2.2 Lid handle ...........................................................................................25
3.2.3 Rotor chamber .....................................................................................25
3.2.4 Instrument status lights ...........................................................................25

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3.3 Internal features of the Rotor-Gene Q MDx ......................................................26
3.3.1 Rotor hub ............................................................................................26
3.3.2 Optical lens .........................................................................................26
Optical lens were the excitation diode light is focused on the tubes.........................26
4Installation Procedures ............................................................................................27
4.1 System delivery and installation......................................................................27
4.1.1 Unpacking the Rotor-Gene Q MDx .........................................................27
4.1.2 Hardware installation............................................................................28
4.1.3 Software installation..............................................................................29
4.1.4 Software version...................................................................................32
4.1.5 Additional software on computers connected to Rotor-Gene Q MDx
instruments .......................................................................................................32
4.2 Site requirements..........................................................................................39
4.3 AC power connection ...................................................................................40
4.3.1 Power requirements ..............................................................................40
4.3.2 Grounding requirements........................................................................40
4.3.3 Installation of AC power cord ................................................................40
4.4Configuration for Windows security................................................................40
4.5 Workstation requirements..............................................................................42
4.6 Unpacking and installing the Rotor-Gene Q MDx .............................................42
4.6.1 Software upgrade.................................................................................43
4.7 Accessories..................................................................................................44
4.8 Repackaging and shipping the Rotor-Gene Q MDx ..........................................44
4.9 Getting started .............................................................................................44
4.9.1 Powering ON the Rotor-Gene Q MDx and workstation .............................44
5Operating Procedures.............................................................................................45
5.1 Use of the Rotor-Gene Q MDx software...........................................................45
5.1.1 Quick Start wizard ...............................................................................45
5.1.2 Advanced wizard.................................................................................49
5.2 Use of the Rotor-Gene Q MDx hardware.........................................................67
5.2.1 Rotor types ..........................................................................................67

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5.2.2 Reaction setup......................................................................................70
5.2.3 Rotor-Disc setup....................................................................................73
6Analysis User Interface............................................................................................77
6.1 Workspace..................................................................................................77
6.2 Toolbar .......................................................................................................77
6.3 View raw channels .......................................................................................77
6.4 Toggling samples .........................................................................................78
6.5 File menu.....................................................................................................80
6.5.1 New ...................................................................................................80
6.5.2 Open and Save....................................................................................81
6.5.3 Reports................................................................................................82
6.5.4 Setup ..................................................................................................83
6.6 Analysis menu..............................................................................................83
6.6.1 Analysis ..............................................................................................83
6.6.2 Quantitation.........................................................................................85
6.6.3 Two standard curve ..............................................................................96
6.6.4 Delta delta CTrelative quantitation........................................................100
6.6.5 Melt curve analysis .............................................................................103
6.6.6 Comparative quantitation ....................................................................106
6.6.7 Allelic discrimination...........................................................................108
6.6.8 Scatter graph analysis.........................................................................109
6.6.9 EndPoint analysis................................................................................111
6.6.10 Concentration analysis ........................................................................117
6.6.11 High Resolution Melt analysis...............................................................120
6.7 Run menu ..................................................................................................121
6.7.1 Start Run............................................................................................121
6.7.2 Pause Run..........................................................................................121
6.7.3 Stop Run............................................................................................122
6.8 View menu ................................................................................................122
6.8.1 Run Settings .......................................................................................122
6.8.2 Temperature Graph ............................................................................125

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6.8.3 Profile Progress ..................................................................................126
6.8.4 Edit Samples......................................................................................127
6.8.5 Display Options .................................................................................132
6.9 Access Protection for Rotor-Gene Q Software.................................................133
6.9.1 Configuration for Windows 7 ..............................................................134
6.9.2 Configuration for Windows 10 ............................................................139
6.9.3 Running multiple users on the same computer.........................................141
6.9.4 Audit trails.........................................................................................142
6.9.5 Run Signatures ...................................................................................144
6.9.6 Sample locking ..................................................................................145
6.9.7 Locked templates ................................................................................147
6.10 Gain menu ............................................................................................147
6.11 Window menu .......................................................................................148
6.12 Help function .........................................................................................148
6.12.1 Send Support E-Mail ...........................................................................149
7Additional Functions .............................................................................................153
7.1 Analysis templates ......................................................................................153
7.2 Opening a second run ................................................................................153
7.3 Scaling options ..........................................................................................153
7.4 Exporting graphs........................................................................................154
7.5 Spanner/wrench icon .................................................................................157
7.6 Selected area options .................................................................................158
8Maintenance .......................................................................................................159
8.1 Cleaning the Rotor-Gene Q MDx surface.......................................................159
8.2 Decontaminating the Rotor-Gene Q MDx surface............................................160
8.3 Rotor-Gene Q repair ...................................................................................160
9Optical Temperature Verification............................................................................161
9.1 OTV principle ............................................................................................161
9.2 Rotor-Disc OTV Kit components ....................................................................161
9.3 Running an OTV.........................................................................................162
10 High Resolution Melt Analysis................................................................................165

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10.1 Instrumentation.......................................................................................166
10.2 Chemistry ..............................................................................................167
10.3 SNP genotyping example ........................................................................167
10.4 Methylation analysis example ..................................................................169
10.5 Guidelines for successful HRM analysis .....................................................170
10.6 Sample preparation................................................................................172
10.7 Software setup .......................................................................................172
10.8 Real-time PCR data analysis.....................................................................178
10.9 HRM data analysis .................................................................................179
11 Troubleshooting ...................................................................................................183
11.1 Log Archives ..........................................................................................184
11.2 Hardware and software errors .................................................................184
11.2.1 HRM troubleshooting ..........................................................................184
11.3 Error and warning messages ...................................................................185
11.3.1 General instrument errors ....................................................................185
11.3.2 Rotor-Gene Q Software messages ........................................................187
12 Glossary .............................................................................................................190
13 Technical Specifications ........................................................................................191
13.1 Environmental conditions – operating conditions ........................................191
13.2 Transportation conditions.........................................................................191
13.3 Storage conditions..................................................................................191
13.4 Mechanical data and hardware features...................................................191
13.5 Specifications (hardware and software).....................................................192
13.5.1 Thermal specifications .........................................................................192
13.5.2 Optical specifications..........................................................................192
14 Appendix A – Legal..............................................................................................193
14.1 FCC Declaration.....................................................................................193
14.2 IEC EN 61326 Compliance.....................................................................194
14.3 Declaration of Conformity........................................................................195
14.4 Waste Electrical and Electronic Equipment (WEEE).....................................196
14.5 Liability Clause.......................................................................................197

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14.6 Software License Agreement ....................................................................198
15 Appendix B – Mathematical Techniques..................................................................201
15.1 Quantitation ..........................................................................................201
15.1.1 Confidence intervals for calculated concentrations..................................201
15.1.2 Confidence intervals for CT values........................................................202
16 Ordering Information............................................................................................203
16.1 Rotor-Gene Q MDx products, accessories, and consumables .......................203
17 Document Revision History ....................................................................................206

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1Introduction
Thank you for choosing the Rotor-Gene Q MDx. We are confident it will become an integral part
of your laboratory.
Before using the Rotor-Gene Q MDx, it is essential that you read this user manual carefully and pay
particular attention to the safety information. The instructions and safety information in the user
manual must be followed to ensure safe operation of the instrument and to maintain the instrument
in a safe condition.
Note that the Rotor-Gene Q MDx comes in multiple configurations. For details, including ordering
information, please see Section 16.
1.1 About this user manual
This user manual provides information about the Rotor-Gene Q MDx in the following sections:
Introduction
Safety Information
General Description
Installation Procedures
Operating Procedures
Maintenance
Troubleshooting
Technical Specifications
Appendices
The appendices contain the following information:
Appendix A – Legal
Appendix B – Mathematical Techniques

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1.2 General information
1.2.1 Technical assistance
At QIAGEN®, we pride ourselves on the quality and availability of our technical support. Our
Technical Services Departments are staffed by experienced scientists with extensive practical and
theoretical expertise in molecular biology and the use of QIAGEN products. If you have any
questions or experience any difficulties regarding the Rotor-Gene Q MDx or QIAGEN products in
general, do not hesitate to contact us.
QIAGEN customers are a major source of information regarding advanced or specialized uses of
our products. This information is helpful to other scientists as well as to the researchers at QIAGEN.
We therefore encourage you to contact us if you have any suggestions about product performance
or new applications and techniques.
For technical assistance, contact QIAGEN Technical Services.
For up-to-date information about the Rotor-Gene Q MDx, visit
https://www.qiagen.com/products/instruments-and-automation/pcr-instruments/rotor-gene-q-mdx/.
Website: support.qiagen.com
When contacting QIAGEN Technical Services about errors, please have the following information
ready:
Rotor-Gene Q MDx serial number, type, and version
Error code (if applicable)
Timepoint when the error occurred for the first time
Frequency of error occurrence (i.e., intermittent or persistent error)
Copy of log files
1.2.2 Policy statement
It is the policy of QIAGEN to improve products as new techniques and components become
available. QIAGEN reserves the right to change specifications at any time. In an effort to produce
useful and appropriate documentation, we appreciate your comments on this user manual. Please
contact QIAGEN Technical Services.

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1.2.3 Version management
This document is the Rotor-Gene Q MDx User Manual , revision R1, for Rotor-Gene Q MDx
instruments using Rotor-Gene Q software version 2.3.x (where x is ≥ 0).
1.3 Intended use of the Rotor-Gene Q MDx
The Rotor-Gene Q MDx instrument is designed to perform real-time thermal cycling, detection,
and/or quantification using the polymerase chain reaction (PCR) in clinical applications.
The Rotor-Gene Q MDx is intended to be used only in combination with QIAGEN kits indicated for
use with Rotor-Gene Q instruments for applications described in the respective QIAGEN kit
handbooks.
If the Rotor-Gene Q MDx instrument is used with other than QIAGEN kits, it is the user’s
responsibility to validate the performance of such product combination for any particular
application.
The Rotor-Gene Q MDx instrument is intended for in vitro diagnostic use.
The Rotor-Gene Q MDx instrument is intended for use by professional users, such as technicians
and physicians trained in molecular biological techniques and the operation of the Rotor-Gene Q
MDx instrument.
1.3.1 Requirements for Rotor-Gene Q MDx
The table below covers the general level of competence and expertise necessary for transportation,
installation, use, maintenance and servicing of the Rotor-Gene Q MDx.
Task Personnel Training and experience
Delivery No special requirements No special requirements
Installation Laboratory technicians or
equivalent
Appropriately trained and experienced personnel
familiar with the use of computers and automation in
general
Routine use (running
protocols)
Laboratory technicians or
equivalent
Professional users, such as technicians or physicians,
trained in molecular biology techniques
Routine maintenance Laboratory technicians or
equivalent
Professional users, such as technicians or physicians,
trained in molecular biology techniques
Servicing and annual
maintenance
QIAGEN Field Service specialists
only
Regularly trained, certified, and authorized by
QIAGEN

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1.4 Materials required
Note: Only use accessories supplied by QIAGEN.
Rotor-Gene Q MDx 5Plex (cat. no. 9002020)
Rotor-Gene Q MDx 5Plex HRM (cat. no. 9002030)
Rotor-Gene Q MDx 6Plex (cat. no. 9002040)
Laptop (cat. no. 9026760)
72-Well Rotor (cat. no. 9018903)
Locking Ring 72-Well Rotor (cat. no. 9018904)
Loading Block 72 x 0.1 ml Tubes (cat. no. 9018901)
Rotor Holder (cat. no. 9018908)
Strip Tubes and Caps, 0.1 ml (250) (cat. no. 981103)
Rotor Gene Q SW (cat. no. 9023241)
1.5 Materials required but not provided
Safety glasses
Gloves
Lab coat
To use the Rotor-Gene Q MDx, a PCR kit is needed but must be purchased separately, to discover
the range of kits available, check QIAGEN.com.

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2Safety Information
Before using the Rotor-Gene Q MDx, it is essential that you read this user manual carefully and pay
particular attention to the safety information. The instructions and safety information in the user
manual must be followed to ensure safe operation of the instrument and to maintain the instrument
in a safe condition.
The following types of safety information appear throughout the
Rotor-Gene Q MDx User Manual .
WARNING The term WARNING is used to inform you about situations that could result in
personal injury to you or others.
Details about these circumstances are given in a box like this one.
CAUTION
The term CAUTION is used to inform you about situations that could result in
damage to an instrument or other equipment.
Details about these circumstances are given in a box like this one.
The guidance provided in this manual is intended to supplement, not supersede, the normal safety
requirements prevailing in the user’s country.
Please be aware that you may be required to consult your local regulations for reporting serious
incidents that have occurred in relation to the device to the manufacturer and/or its authorized
representative and the regulatory authority in which the user and/or the patient is established.

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2.1 Proper use
WARNING Risk of personal injury and material damage
Improper use of the Rotor-Gene Q MDx may cause personal injuries or damage
to the instrument.
The Rotor-Gene Q MDx must only be operated by qualified personnel who have
been appropriately trained.
Servicing of the Rotor-Gene Q MDx instrument must only be performed by a
QIAGEN Field Service Specialist.
Perform the maintenance as described in Section 8. QIAGEN charges for repairs that are required
due to incorrect maintenance.
WARNING Risk of personal injury and material damage
The Rotor-Gene Q MDx is too heavy to be lifted by one person. To avoid
personal injury or damage to the instrument, do not lift the instrument alone.
Contact QIAGEN Technical Services to relocate the instrument.
WARNING Risk of personal injury and material damage
Do not attempt to move the Rotor-Gene Q MDx during operation.
CAUTION
Damage to the instrument
Avoid spilling water or chemicals onto the Rotor-Gene Q MDx. Damage caused
by water or chemical spillage will void your warranty.
Note: In case of emergency, switch off the Rotor-Gene Q MDx at the power switch at the back of
the instrument and unplug the power cord from the power outlet.

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CAUTION
Risk of personal injury and material damage
Do not try to open the lid during an experiment, or while the Rotor-Gene Q MDx
is spinning. Otherwise, if you overcome the lid lock and reach inside, you risk
contact with parts that are hot, electrically live, or moving at high speed, and
you may injure yourself and damage the instrument.
CAUTION
Risk of personal injury and material damage
If you need to stop an experiment quickly, turn off the power to the instrument,
then open the lid. Let the chamber cool before reaching inside. Otherwise you
risk injury by touching parts that are hot.
CAUTION
Risk of personal injury and material damage
If the equipment is used in a manner not specified by the manufacturer, the
protection provided by the equipment may be impaired.
CAUTION
Risk of personal injury and material damage
Loose paper underneath the Rotor-
Gene Q MDx interferes with instrument
cooling. It is recommended that the area beneath the instrument is kept free of
clutter.
CAUTION
Damage to the instrument
Always use a locking ring on the rotor. This stops caps from coming off tubes
during an experiment. If caps come off during an experiment, they may damage
the chamber.

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CAUTION
Risk of material damage
Visually inspect and make sure the rotor is not damaged or deformed before
each run.
If you touch the Rotor-Gene Q MDx during an experiment, while you are charged with static
electricity, in severe cases the Rotor-Gene Q MDx may reset. However, the software will restart the
Rotor-Gene Q MDx and continue the experiment.
2.2 Electrical safety
Disconnect the line power cord from the power outlet before servicing.
WARNING Electrical hazard
Any interruption of the protective conductor (earth/ground lead) inside or
outside the instrument or disconnection of the protective conductor terminal is
likely to make the instrument dangerous.
Intentional interruption is prohibited.
Lethal voltages inside the instrument
When the instrument is connected to line power, terminals may be live and
opening covers or removing parts is likely to expose live parts.
To ensure satisfactory and safe operation of the Rotor-Gene Q MDx, follow the advice below:
The line power cord must be connected to a line power outlet that has a protective conductor
(earth/ground).
Do not adjust or replace internal parts of the instrument.
Do not operate the instrument with any covers or parts removed.
If liquid has spilled inside the instrument, switch off the instrument, disconnect it from the
power outlet, and contact QIAGEN Technical Services.
If the instrument becomes electrically unsafe, prevent other personnel from operating it, and contact
QIAGEN Technical Services.

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The instrument may be electrically unsafe when:
It or the line power cord appears to be damaged.
It has been stored under unfavorable conditions for a prolonged period.
It has been subjected to severe transport stresses.
WARNING Electrical hazard
The instrument has an electrical compliance label which indicates the voltage
and frequency of the power supply as well as fuse ratings. The equipment should
only be operated under these conditions.
2.3 Biological safety
Specimens and reagents containing materials from biological sources should be treated as
potentially infectious. Use safe laboratory procedures as outlined in publications such as
Biosafety
in Microbiological and Biomedical Laboratories
, HHS (https://www.cdc.gov/labs/BMBL.html).
Samples
Samples may contain infectious agents. You should be aware of the health hazard presented by
such agents and should use, store, and dispose of such samples according to the required safety
regulations.

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WARNING Samples containing infectious agents
Some samples used with this instrument may contain infectious agents. Handle
such samples with the greatest of care and in accordance with the required
safety regulations.
Always wear safety glasses, 2 pairs of gloves, and a lab coat.
The responsible body (e.g., laboratory manager) must take the necessary
precautions to ensure that the surrounding workplace is safe, and that the
instrument operators are suitably trained and not exposed to hazardous levels
of infectious agents as defined in the applicable Safety Data Sheets (SDSs) or
OSHA,* ACGIH,†or COSHH‡documents.
Venting for fumes and disposal of wastes must be in accordance with all
national, state, and local health and safety regulations and laws.
* OSHA: Occupational Safety and Health Administration (United States of America).
†ACGIH: American Conference of Government Industrial Hygienists (United States of America).
‡COSHH: Control of Substances Hazardous to Health (United Kingdom).
2.4 Chemical safety
WARNING Hazardous chemicals
Some chemicals used with this instrument may be hazardous or may become
hazardous after completion of the protocol run. Always wear safety glasses,
gloves, and a lab coat. The responsible body (e.g., laboratory manager) must
take the necessary precautions to ensure that the surrounding workplace is safe
and that the instrument operators are not exposed to hazardous levels of toxic
substances (chemical or biological) as defined in the applicable Safety Data
Sheets (SDSs) or OSHA,* ACGIH†or COSHH‡documents.
Venting for fumes and disposal of wastes must be in accordance with all
national, state, and local health and safety regulations and laws.
* OSHA: Occupational Safety and Health Administration (United States of America).
†ACGIH: American Conference of Government Industrial Hygienists (United States of America).
‡COSHH: Control of Substances Hazardous to Health (United Kingdom).

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Toxic fumes
If working with volatile solvents or toxic substances, you must provide an efficient laboratory
ventilation system to remove vapors that may be produced.
2.5 Waste disposal
Used labware may contain hazardous chemicals. Such wastes must be collected and disposed of
properly according to local safety regulations.
For more information about how to dispose of the Rotor-Gene Q MDx, see “Waste Electrical and
Electronic Equipment (WEEE)”, page 196.
2.6 Mechanical hazards
The lid of the Rotor-Gene Q MDx must remain closed during operation of the instrument.
WARNING Moving parts
To avoid contact with moving parts during operation of the Rotor-Gene Q MDx,
the instrument must be operated with the lid closed.
WARNING Risk of personal injury and material damage
Open and close the lid of the Rotor-Gene Q MDx carefully to avoid trapping
fingers or clothing.
WARNING Damage to the instrument
Make sure that the rotor and locking ring are installed correctly. If the rotor or
locking ring show signs of mechanical damage or corrosion do not use the
Rotor-Gene Q MDx; contact QIAGEN Technical Services.

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WARNING Damage to the instrument
When Rotor-Gene Q MDx is started immediately after delivery in cold climates,
mechanical parts can block.
Allow the instrument to acclimatize to room temperature for at least an hour
before turning the instrument on.
WARNING Damage to the instrument
In case of breakdown caused by power failure, remove the power cord and
wait 10 min before attempting to manually open the lid.
WARNING Risk of overheating
To ensure proper ventilation, maintain a minimum clearance of 10 cm at the
sides and rear of the Rotor-Gene Q MDx.
Slits and openings that ensure the ventilation of the Rotor-Gene Q MDx must not
be covered.
Heat hazard
WARNING Hot surface
The Rotor-Gene Q MDx chamber can reach tempe
ratures above 120°C
(248°F). Avoid touching it when it is hot.
WARNING Hot surface
When pausing a run, the Rotor-Gene Q MDx will not be cooled completely to
room temperature. Exercise caution before handling the rotor or any tubes in
the instrument.

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2.7 Maintenance safety
Perform the maintenance as described in Section 8. QIAGEN charges for repairs that are required
due to incorrect maintenance.
WARNING
/CAUTION
Risk of personal injury and material damage
Only perform maintenance that is specifically described in this user manual.
WARNING Risk of fire
When cleaning the Rotor-Gene Q MDx with alcohol-based disinfectant, leave
the Rotor-Gene Q MDx door open to allow flammable vapors to disperse.
WARNING
/CAUTION
Risk of electric shock
Do not disassemble the Rotor-Gene Q MDx instrument.
CAUTION Damage to the instrument housing
Never clean the instrument housing with alcohol or alcohol-based solutions.
Alcohol will damage the housing. To clean the housing, use distilled water
only.