Qiagen GeneReader User manual

Sample to Insight__
December 2017
QIAGEN
GeneReader
User Manual
For use with Advanced Process Flow (APF/HP) Instrument
Configuration and GeneReader™ Software version 1.6
For Research Use Only. Not for use in diagnostic procedures.

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
12/2017
2
Contents
Instrument Configuration History ...........................................................................................6
1 Introduction .............................................................................................................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
1.3 Intended use of the GeneReader .......................................................................9
1.4 Requirements for GeneReader users ................................................................10
2 Safety Information ..................................................................................................11
2.1 Proper use ...................................................................................................12
2.2 Electrical safety ............................................................................................14
2.3 Environment .................................................................................................15
2.3.1 Operating conditions ............................................................................15
2.4 Chemicals....................................................................................................16
2.5 Waste disposal ............................................................................................16
2.6 Mechanical hazards .....................................................................................17
2.7 Maintenance safety ......................................................................................17
2.8 Symbols on the GeneReader ..........................................................................18
3 General Description ...............................................................................................20
3.1 QIAGEN GeneReader Sample to Insight NGS workflow .................................20
3.2 GeneReader principle ...................................................................................21
3.3 External features of the GeneReader ...............................................................22
3.3.1 Status lights ..........................................................................................22
3.3.2 Flow Cell door .....................................................................................22
3.3.3 Hood ..................................................................................................23
3.3.4 Fluidic drawer ......................................................................................24
3.3.5 USB ports ............................................................................................24
3.3.6 Power switch ........................................................................................24
3.3.7 Power cord socket ................................................................................24

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
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3.3.8 Cooling air outlet..................................................................................24
3.3.9 Workstation equipment .........................................................................25
3.4 Internal features of the GeneReader ................................................................25
3.4.1 GeneReader Flow Cell ..........................................................................25
4 Installation Procedures ............................................................................................27
4.1 System delivery and installation ......................................................................27
4.2 Site requirements ..........................................................................................27
4.3 AC Power and USB cable connections ............................................................28
4.3.1 Power requirements ..............................................................................28
4.3.2 Grounding requirements ........................................................................29
4.3.3 Installation of AC power cords, USB cables and workstation .....................29
4.3.4 Installation of AC power cords, USB cables and workstation using an
optional UPS ....................................................................................................29
4.4 Workstation requirements ..............................................................................30
4.5 Getting started .............................................................................................31
4.5.1 Powering ON the GeneReader and workstation .......................................31
4.5.2 Software upgrade .................................................................................32
5 Operating Procedures .............................................................................................34
6 GeneReader Software ............................................................................................35
6.1 Use of the GeneReader software ....................................................................35
6.1.1 Start-up ...............................................................................................35
6.1.2 Software workflow ................................................................................35
6.1.3 User interface .......................................................................................36
6.1.4 Status of Flow Cells view .......................................................................37
6.1.5 Status of Fluids view ..............................................................................38
6.1.6 Status of Configuration view ..................................................................39
6.1.7 File handling ........................................................................................41
6.2 Workflow procedures ...................................................................................41
6.2.1 Flow Cell setup .....................................................................................41
6.2.2 Loading and running the GeneReader .....................................................43
6.2.3 Staggered loading of Flow Cells ............................................................43

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HP
) Instrument Configuration
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6.2.4 Unloading reagents and Flow Cells ........................................................43
6.2.5 Run finished .........................................................................................43
7 Maintenance .........................................................................................................48
7.1 Equipment and reagents to be supplied by user ...............................................48
7.2 Maintenance wash .......................................................................................48
7.2.1 Routine maintenance (DI water wash) ......................................................48
7.2.2 Weekly maintenance ............................................................................51
7.2.3 Preparing the GeneReader fluidics lines for long-term storage ....................58
7.2.4 Monthly cleaning procedure ..................................................................59
7.3 General cleaning procedures .........................................................................59
7.3.1 Cleaning agents ...................................................................................59
7.3.2 General instructions ..............................................................................60
7.3.3 Servicing .............................................................................................61
7.4 Cleaning the workstation hard disk .................................................................61
7.4.1 Procedure ............................................................................................61
7.5 Creating a service archive folder for troubleshooting ........................................62
7.5.1 Procedure ............................................................................................62
8 Troubleshooting .....................................................................................................64
8.1 Hardware and software errors .......................................................................64
8.1.1 Application module ..............................................................................64
8.1.2 Manage Files module ............................................................................64
8.1.3 Flow Cells ............................................................................................65
8.1.4 Run module ..........................................................................................65
8.1.5 Start Run module ..................................................................................65
9 Technical Data .......................................................................................................66
9.1 Environmental conditions – operating conditions ..............................................66
9.2 Mechanical data and hardware features .........................................................66
9.3 Workstation specifications (hardware and software) .........................................66
9.3.1 Workstation .........................................................................................66
9.3.2 Software ..............................................................................................67
Appendix A .....................................................................................................................68

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
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Declaration of Conformity .......................................................................................68
License Terms .........................................................................................................69
Waste Electrical and Electronic Equipment (WEEE) ....................................................70
FCC Declaration ....................................................................................................71
Liability Clause ......................................................................................................72
Appendix B .....................................................................................................................73
Ordering Information ..............................................................................................73
Appendix C .....................................................................................................................74
Safety Information Translated into German and French ...............................................74
Sicherheitsinformationen ....................................................................................74
Informations de Sécurité .....................................................................................74
Index ............................................................................................................................86

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
12/2017
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Instrument Configuration History
Document title
Document
number Date
Description of changes and
specifications
Compatible software and
sequencing kits
QIAGEN
GeneReader
User Manual
for use with
APF/HP
Instrument
Configuration
HB 2503
001
December 2017 Supports Advanced Process
Flow (APF) workflow and UMI
Advanced (HP) chemistry
compatible with:
•GeneRead
™
QIAact
Actionable Insights Tumor
Panel, cat. no. 181910
•GeneRead QIAact BRCA 1/2
Panel, cat. no. 181920
•GeneRead QIAact Lung DNA
UMI Panel, cat. no. 181931
•GeneRead QIAact Lung
Fusion UMI Panel, cat. no.
181936
•Any future GeneRead QIAact
panel with UMI technology
Updated the following
specifications:
•Higher data output, >7%
•Enhanced maintenance wash
procedure
GeneReader instruments
released prior to the Advanced
Process Flow instrument
configuration can be upgraded
to the APF/HP instrument
configuration.
GeneReader Software
version 1.6
QIAGEN GeneRead UMI
Advanced Sequencing Q Kit
(3), cat. no. 185251, which
consists of:
•GeneRead UMI
Advanced Sequencing Q
Add-Ons (3), cat. no.
1108488
•GeneRead UMI
Advanced Sequencing Q
Flow Cell (3), cat. no.
1108489
•GeneRead UMI
Advanced Sequencing Q
Buffers (3), cat. no.
1108487
GeneRead UMI Advanced
Sequencing Q Wash Buffers
(9), cat. no. 185905,
purchased separately

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
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Document title
Document
number Date
Description of changes and
specifications
Compatible software and
sequencing kits
QIAGEN
GeneReader
User Manual
for use with
APF Instrument
Configuration
HB-2325-
001
December 2016 Supports Advanced Process
Flow (APF) workflow compatible
with:
• GeneRead
™
QIAact
Actionable Insights Tumor
Panel, cat. no. 181910
• GeneRead QIAact Lung
DNA Panel, cat. no.
181930
• GeneRead QIAact BRCA
1/2 DNA Panel
Updated the following
specifications:
•Higher read length, >30%
•Higher data output, >50%
•Higher sample
multiplexing capacity per
flow cell for the GeneRead
QIAact Actionable Insights
Tumor Panel (ATP)
•Approximately 20% less
reagent consumption per
cycle
•Equal or less sequencing
time
•Parallel or staggered
processing of up to 3 flow
cells
GeneReader instruments
released prior to the Advanced
Process Flow instrument
configuration can be upgraded
to the APF instrument
configuration
GeneReader Software
version 1.4.0
QIAGEN GeneRead
Advanced Sequencing Q Kit
(3), cat. no. 185231
GeneRead Sequencing Buffer
Q Kit (16), cat. no. 185901
IMPORTANT: When used in
combination with the
QIAGEN GeneRead
Advanced Sequencing Q Kit,
the GeneRead Sequencing
Buffer Q Kit (16) will allow
the user to process 6 Flow
Cells.
GeneReader
User Manual
HB-2023-
001
December 2015 Specifications:
•Compatible with
GeneRead QIAact Panels,
Powered by QCI™, cat.
no. 181910
•Approximately 45 hours
sequencing time
•Parallel or staggered
processing of up to 4 Flow
Cells
GeneReader Software up to
version 1.1.3
GeneRead Sequencing Q Kit
(1), cat. no. 185200
GeneRead Sequencing Q Kit
(4), cat. no. 185201
GeneRead Sequencing Buffer
Q Kit, (16) cat. no. 185901

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
12/2017
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1Introduction
Thank you for choosing the GeneReader. We are confident it will become an integral part of your
laboratory.
Before using the GeneReader, 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.
1.1 About this user manual
This user manual provides information about the GeneReader in the following sections:
 Instrument Configuration History
 Introduction
 Safety Information
 General Description
 Installation Procedures
 Operating Procedures
 Maintenance
 Troubleshooting
 Technical Data
 Appendices
 Index
The appendices contain the following information:
 Declaration of Conformity
 License Terms
 Waste Electrical and Electronic Equipment (WEEE)
 FCC Declaration
 Liability Clause
 GeneReader Accessories
 Safety Information Translated into German and French

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HP
) Instrument Configuration
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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 GeneReader 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 (see back cover).
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 (see back cover).
1.3 Intended use of the GeneReader
The GeneReader is designed to perform next-generation sequencing (NGS) applications by
integrating highly parallel fluorescence-based sequencing chemistry with detection of the
corresponding fluorescent signals from templates that have been clonally amplified using the
GeneRead QIAcube .
GeneReader software provides a wizard for setting up the sequencing, data storage management,
and the functionality for base calling and generation of FASTQ files.
The GeneReader is intended to be used only in combination with QIAGEN kits indicated for use
with the GeneReader for applications described in the respective QIAGEN kit product sheets or
handbooks.
The GeneReader is intended for Research Use Only. Not for use in diagnostic procedures.

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
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The GeneReader is intended for use by professional users trained in molecular biological techniques
and in the operation of the GeneReader.
1.4 Requirements for GeneReader users
Table 1covers the general level of competence and training necessary for transportation,
installation, use, maintenance and servicing of the GeneReader.
Table 1. Recommended training and skill proficiency to use, maintain and service GeneReader.
Task Personnel Training and experience
Transportation No special requirements No special requirements
Installation QIAGEN Field Service Specialists
only
Special training required
System relocation QIAGEN Field Service Specialists
only
Special training required
Routine use (running protocols) Laboratory technicians or equivalent Appropriately trained and experienced
personnel familiar with use of
computers and automation in general
Regular and weekly maintenance Laboratory technicians or equivalent Appropriately trained and experienced
personnel familiar with use of
computers and automation in general
Annual preventative maintenance and
servicing
QIAGEN Field Service Specialists
only
Special training required

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
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2Safety Information
Before using the GeneReader, 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 condition
of the instrument to ensure its continued safe operation.
IMPORTANT: safety information in German (Sicherheitsinformationen) and French (Informations
de Sécurité) is provided in Appendix C, page 74.
The following types of safety information appear throughout the QIAGEN GeneReader User Manual
for Advanced Process Flow APF/HP) Instrument Configuration.
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.

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HP
) Instrument Configuration
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2.1 Proper use
WARNING Risk of personal injury and material damage
(W1)
Improper use of the GeneReader may cause personal injuries or damage to the
instrument.
The GeneReader must only be operated by qualified personnel who have been
appropriately trained.
Servicing of the GeneReader instrument must only be performed by a QIAGEN
Field Service Specialist.
Perform the maintenance as described in Section 7. QIAGEN charges for repairs that are required
due to incorrect maintenance.
WARNING Risk of personal injury and material damage (W2)
The GeneReader 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 (W3)
Do not attempt to move the GeneReader during operation.
WARNING Risk of personal injury and material damage (W4)
Load flow cell only in accordance with step-by-step instructions provided by
GeneReader software. Beware of moveable parts.
WARNING Risk of personal injury and material damage
(W5)
Do not stare into the beam of the flow cell bar code reader.

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
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CAUTION
Risk of material damage (C1)
Avoid moving the workbench and causing vibrations to the GeneReader during
operation to prevent disturbing sensitive optical measurements.
CAUTION
Damage to the instrument (C2)
Avoid spilling water or chemicals onto the GeneReader. Damage caused by
water or chemical spillage will void your warranty.
CAUTION
Risk of material damage (C3)
Do not place any items on top of the instrument.
In case of emergency, power OFF the GeneReader using the power switch at the right, rear panel
of the instrument and unplug the power cord from the power outlet.
CAUTION
Damage to the instrument (C4)
Only use QIAGEN consumables with the GeneReader. Damage caused by use
of other types of consumables will void your warranty.
CAUTION
Damage to the instrument (C5)
Make sure that the flow cell is inserted in the correct position. Incorrect insertion
of the flow cell can damage the instrument.
WARNING Fire hazard (W6)
Empty the liquid waste bottle before each run and make sure to place it in the
correct orientation back in the GeneReader instrument. Spilling of liquid-waste
may cause an electrical short-circuit and fire.

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HP
) Instrument Configuration
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2.2 Electrical safety
Disconnect the line power cord from the power outlet before servicing.
WARNING Electrical hazard (W7)
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 strongly discouraged as doing so may
result in electric shock or death.
WARNING Damage to electronics (W8)
Before powering ON the instrument make sure that the correct supply voltage
is used.
Incorrect use of supply voltage may cause damage to electronics.
See specifications indicated on the type plate of the instrument.
WARNING Risk of electric shock (W9)
Do not open any panels on the GeneReader.
Risk of personal injury and material damage
Only perform maintenance that is specifically described in this user manual.

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HP
) Instrument Configuration
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To ensure satisfactory and safe operation of the GeneReader, follow the advice below:
 The line power cord must be connected to a line power outlet that has a protective conductor
(earth/ground).
 Place instrument in a location so that the power cord is accessible and can be
connected/disconnected.
 Use only the power cord delivered by QIAGEN.
 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 (see back cover).
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.
2.3 Environment
2.3.1 Operating conditions
WARNING Explosive atmosphere (W10)
The GeneReader is not designed for use in an explosive atmosphere.
WARNING Risk of explosion (W11)
The GeneReader is intended for use with reagents and substances supplied with
QIAGEN kits. Use of other reagents and substances may lead to fire or
explosion.

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HP
) Instrument Configuration
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CAUTION
Damage to the instrument (C6)
Direct sunlight may bleach parts of the instrument and cause damage to plastic
parts.
The GeneReader must be located out of direct sunlight.
2.4 Chemicals
WARNING Hazardous chemicals (W12)
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).
2.5 Waste disposal
Used labware may contain hazardous chemicals. Waste must be collected and disposed of
properly according to local safety regulations.
For more information about how to dispose of the GeneReader instrument, see “Waste Electrical
and Electronic Equipment (WEEE)” in Appendix A, page 70.

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HP
) Instrument Configuration
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WARNING Hazardous chemicals and infectious agents
(W13)
The waste contains samples and reagents. This waste may contain toxic or
infectious material and must be disposed of properly. Refer to your local safety
regulations for proper disposal procedures.
2.6 Mechanical hazards
The door of the GeneReader must remain closed during operation of the instrument. Only handle
the flow cell loading station when the flow cell door has been released by the software.
Note: Only power OFF the instrument if the process has been properly terminated by the
software and the flow cell door is closed.
WARNING Moving parts (W14)
To avoid contact with moving parts during operation of the GeneReader, the
instrument must be operated with the flow cell door closed.
If the door sensor is not functioning correctly, contact QIAGEN Technical
Services.
WARNING Risk of overheating (W15)
To ensure proper ventilation, maintain a minimum clearance of 10 cm at the
sides and rear of the GeneReader.
Slits and openings that ensure the ventilation of the GeneReader must not be
covered.
2.7 Maintenance safety
WARNING Risk of personal injury and material damage
(W16)
Only perform maintenance that is specifically described in this user manual.

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
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CAUTION
Damage to the instrument (C7)
Do not use bleach, solvents, or reagents containing acids, alkalis, or abrasives
to clean the GeneReader.
2.8 Symbols on the GeneReader
Symbol Location Language Description
Inside instrument – Heat hazard – do not perform
maintenance before the system has
cooled down.
On the instrument – Mechanical hazard – avoid contact
with moving parts.
On front of the
instrument, open
door
– Mechanical hazard – avoid contact
with moving parts.
Inside instrument – Electric shock hazard
On the
instrument, right
side panel
EN This product contains a class 2
laser. Do not stare into the beam.
On the
instrument, right
side panel
FR This product contains a class 2
laser. Do not stare into the beam.
On front of the
instrument, open
door
– This product contains a class 2
laser. Do not stare into the beam.
Type plate on the
right side panel
– WEEE about the disposal of waste
electrical and electronic equipment
for Europe and rest of the world.
Type plate on the
right side panel
– Legal manufacturer.

QIAGEN GeneReader User Manual for Advanced Process Flow (APF/
HP
) Instrument Configuration
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Symbol Location Language Description
On the
instrument, right
side panel
– Consult instructions for use.
On the
instrument, right
side panel
EN Disconnect power supply before
servicing.
Inside instrument – Earth (Ground)
Type plate on the
back of the
instrument
– CE mark for Europe
Type plate on the
back of the
instrument
– FCC mark of the United States
Federal Communications
Commission
Type plate on the
back of the
instrument
– RCM (former C-Tick) for Australia
(supplier identification N17965)
Type plate on the
back of the
instrument
– RoHS mark for China (the restriction
of the use of certain hazardous
substances in electrical and
electronic equipment)
Type plate on the
back of the
instrument
– Instrument serial number
Type plate on the
back of the
instrument
– Certification mark
Indicates that the product was tested
and has met the certification
requirements for electrical, plumbing
and/or mechanical products
Sticker on the
instrument, right
side panel
– Sticker indicating GeneReader with
Advanced Process Flow (APF) and
UMI Advanced (HP) instrument
configuration
SN

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HP
) Instrument Configuration
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3General Description
The QIAGEN GeneReader performs fully automated next-generation sequencing (NGS) by
integrating highly parallel fluorescence-based sequencing chemistry with detection of the
corresponding fluorescent signals on templates that have been clonally amplified using the
GeneRead QIAcube.
The GeneReader sequencer consists of the GeneReader, the workstation, the GeneReader software
and a handheld bar code scanner that connects to the workstation for scanning bar codes of kits
and buffers, which are then automatically entered into the GeneReader software. The initial software
installation is performed by a QIAGEN Field Service Specialist. There are two USB connections
between the GeneReader instrument and workstation. The GeneReader sequencer includes several
additional components, which are listed in Section 4.1.
The GeneReader software provides a FASTQ file of sequence information for each analyzed sample
that is ready for QCI Analyze or GeneRead Link. QCI Analyze automatically runs an optimized
workflow for GeneReader panels and generates a VCF result file that is ready for upload to QCI
Interpret.
3.1 QIAGEN GeneReader Sample to Insight NGS workflow
The QIAGEN GeneReader Sample to Insight workflow provides a streamlined and standardized
approach to next-generation sequencing (NGS), from sample preparation to the biological
interpretation of sequencing data.
The majority of the workflow is automated, ensuring greater standardization and more accurate
results.
QIAGEN Clinical Insight™ combines analytical tools and integrated human disease content,
providing access to current and advanced interpretations of genomic data. QCI Analyze or
GeneRead Link automatically sends samples through predefined workflows and provides a web-
based result viewer. Afterwards, QCI Interpret (another web-based viewer) provides a biological
interpretation.