Agilent Technologies Magnis NGS Prep System User manual

Magnis/Magnis Dx NGS Prep System
User Guide
Magnis Dx NGS Prep System, P/N K1007AA: For In Vitro Diagnostic Use
Magnis NGS Prep System, P/N G9710AA: For Research Use Only. Not for use in diagnostic procedures.
Revision A0, June 2019

Magnis and Magnis Dx NGS Prep System User Guide 2
Symbol Table
Safety Notices
CAUTION
A CAUTION notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if
not correctly performed or adhered to, could result in damage to the product or loss of important data. Do
not proceed beyond a CAUTION notice until the indicated conditions are fully understood and met.
A WARNING notice denotes a hazard.
A WARNING notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that,
if not correctly performed or adhered to, could result in personal injury or death. Do not proceed beyond a
WARNING notice until the indicated conditions are fully understood and met.
European Conformity Caution
In Vitro Diagnostic Medical Device CSA mark
Manufacturer Consult Instructions for Use
Manufacture date Do not discard in domestic household
waste
Caution, hot surfaces Caution, pinching hazard
Environmentally Friendly Use Period
(EFUP) of 40 years Caution, ultra-violet light
Authorized representative in the
European Community Earth ground
WARNING

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Content
1 Before You Begin 7
Product Description 8
Intended Use 8
Principle of the NGS Prep Procedure 8
Limitations of Use 8
Instrument Specifications 9
Materials Provided 10
Optional Accessories 10
Optional Cleaning Supplies 10
Product Inspection 11
Safety Precautions 11
Environmental Requirements 13
Installation Requirements 13
2 Hardware Overview 14
Instrument Components 15
Instrument Status Indicator Lights 18
3 Getting Started 19
Starting Up the Magnis/Magnis Dx NGS Prep System 20
Turn on the instrument 20
Log in to the system 20
Managing User Accounts 22
About user access levels 22
Add new user accounts 22
Edit user accounts 24
Disable user accounts 25
Programming System Settings 27
Set the chiller temperature 27
Set the time and date 27
Assign an instrument name 28
View the instrument serial number and software version 29
Set up the instrument IP address 29
Set the instrument health check settings 30
Setting Up Email Alerts and Protocol Alerts 32
Set up the email settings for outgoing email alerts 32
Set up alerts for notification of new protocols 33

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4 Operating the System 34
Running Protocols 35
Prepare the instrument for running a protocol 35
Prepare the reagents and plasticware 35
Set up and initiate the protocol run 36
Collect final library samples and clean up the system 37
Running and Viewing Diagnostic Tests 38
Perform instrument diagnostic tests 38
View reports for diagnostic tests and instrument health checks 39
Decontaminating with UV Light 41
Run a decontamination “quick cycle” 41
Run a UV decontamination “extended cycle” 42
Running Auto-Teaching and Teach-Point Verification 43
Run auto-teaching 43
Include teach-point verification in the IHC 44
Installing Updates 45
Install protocol updates 45
Install firmware updates 47
5 Performing Maintenance 49
Annual Preventative Maintenance 50
Cleaning the System Components 51
Precautions to take when cleaning the system components 51
Clean the deck surfaces and instrument exterior 51
Clean the barcode scanner 52
Replacing the UV Tube and Viewing UV Tube Usage 53
Request a UV tube replacement 53
View usage hours for the UV tube 53
Disposing of Instrument Parts 54
6 Software User Interface Reference 55
Software User Interface Overview 56
Login screen 58
Home screen 59
Settings screens 60
Settings screen 60
User Management screen 61
Add New User screen 62

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Edit User screen 63
System Settings screen 64
Export Files screen 65
Protocols screen 66
Protocol Update screen 67
Connectivity Settings screen 68
Auto Teach screen 69
Hardware Usage Tracking screen 69
Instrument Diagnostic screen 70
System Settings screens 72
Instrument Settings screen 72
Date & Time Settings screen 73
Chiller Setting screen 74
Firmware Update screen 74
Connection Settings screen 75
Other Settings screen 76
Instrument Diagnostic screens 78
Diagnostic Test screen 78
Diagnostic Test Report screen 79
Diagnostic Report Explorer screen 80
Decontamination screen 81
Run Data Explorer screen 82
Post Run Data screen 83
Run Setup tab 83
Run Info tab 84
Labware Info tab 84
Audit Trails tab 85
Protocol Wizard screens 86
Connectivity Settings screens 87
Email Alert Settings screen 87
Protocol Alert Settings screen 88
Run screens 89
Run screen when run is in-progress 89
Run screen when run is complete 90
Run screen when sample collection is in-progress 90
Run screen when libraries are ready 91
7 Troubleshooting 93
Troubleshooting Suggestions 94

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Magnis system issues 94
Library/sequencing issues 95

Magnis/Magnis Dx NGS Prep System
User Guide
7
1 Before You Begin
Product Description 8
Intended Use 8
Principle of the NGS Prep Procedure 8
Limitations of Use 8
Instrument Specifications 9
Materials Provided 10
Optional Accessories 10
Optional Cleaning Supplies 10
Product Inspection 11
Safety Precautions 11
Environmental Requirements 13
Installation Requirements 13
This chapter contains information for you to read and understand before you start.

Magnis and Magnis Dx NGS Prep System User Guide 8
Product Description
The Magnis NGS Prep System is an automated liquid handling system for next generation
sequencing library preparation and/or target enrichment of human nucleic acid samples.
Intended Use
The Magnis Dx NGS Prep System is an automated liquid handling system for next generation
sequencing library preparation and/or target enrichment of human nucleic acid samples.
The Magnis Dx NGS Prep System is to be used only by operators trained in laboratory techniques
and procedures.
The customer is responsible for validation of assays and compliance with regulatory
requirements that pertain to their procedures and uses of the instrument.
Principle of the NGS Prep Procedure
The Agilent Magnis/Magnis Dx NGS Prep System is a liquid handler that offers start-to-finish
automation of library preparation and target enrichment protocols for next generation sequencing
(NGS). The starting material is fragmented genomic DNA (gDNA) purified from a cell or tissue
sample, blood sample, or formalin-fixed paraffin-embedded (FFPE) sample. The end result is a
target-enriched DNA library ready for sequencing.
The hardware components make up the instrument. See “Instrument Components” on page 15
for a list of these components.
The instrument is controlled through the software component of the system, which is displayed
and operated through the LCD touchscreen. Chapter 3, “Getting Started,” and Chapter 4,
“Operating the System,” include instructions on setting up and operating the Magnis/Magnis Dx
NGS Prep System using the software. Chapter 6, “Software User Interface Reference,” provides a
description of each individual software screen, detailing the purpose of each feature on the
screen.
Limitations of Use
The Magnis/Magnis Dx NGS Prep System has been validated for use with Agilent Magnis NGS
kits.

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Instrument Specifications
* The listed conditions apply to instrument operation. Conditions required for assay performance may
differ.
Table 1 Technical specifications of the instrument
System Component Specification
Thermal cycler module
Minimum temperature of thermal block 4°C
Maximum temperature of thermal block 99°C
Heater/Shaker/Magnet module
Heater Temperature maximum 75°C
Shaker Maximum speed (rpm) 1800 rpm ±5%
Chiller module
Temperature range 4–12°C
Power inlet
AC voltage 100–240 VAC
AC frequency 50/60 Hz
Maximum power 1000 W
System
Acoustic sound pressure 70 dBA
Dimensions, instrument door closed (Height × Depth × Width) 71 cm × 72 cm × 62 cm
Dimensions, instrument door open (Height × Depth × Width) 107 cm × 72 cm × 62 cm
Weight 95 kg
Environmental conditions*
Temperature Operating: 15°C to 25°C
Transport and storage: –40°C to 70°C
Humidity Operating: 30% to 70%, non-condensing
Altitude 2000 m

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Materials Provided
Optional Accessories
If desired, you can use the USB ports on the front of the instrument to connect optional
accessories. Do not use the USB ports as a charging port for phones or other devices.
* Magnis instruments are not compatible with encrypted USB disks.
Optional Cleaning Supplies
You can use the cleaning materials listed below to manually clean the instrument. See “Cleaning
the System Components” on page 51 for instructions.
Table 2 Materials provided with the Magnis/Magnis Dx NGS Prep System
Materials
Instrument with preloaded touchscreen software
Power cord
Functional test certificate
USB disk with PDFs of the User Guide and Quick Reference Guide
Table 3 Optional accessories for use with the system
Description Purpose
Mouse with USB connector For interacting with the touchscreen software
Keyboard with USB connector For interacting with the touchscreen software
USB disk* For transferring files to and from the system
Table 4 Optional supplies for cleaning the system instrument
Description Purpose Vendor
Dilute bleach (10%) wipes Surface-cleaning of the instrument
exterior and instrument deck
Hype-Wipe Bleach
Towelettes, or equivalent
Alcohol (70%) wipes Surface-cleaning of the instrument
exterior and instrument deck
VWR Pre-Moistened Clean
Wipes, or equivalent
Dry, lint-free, scratch-free
wipers
Surface-cleaning of the barcode scanner
window
Kimwipes, or equivalent

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Product Inspection
Upon receipt of the Magnis/Magnis Dx NGS Prep System, carefully inspect the product box for
any visible signs of damage. If damage to the product box is detected, contact Agilent Worldwide
Technical Support.
Allow the shipping container for the Magnis/Magnis Dx NGS Prep System to come to room
temperature prior to unpacking.
Safety Precautions
The Magnis/Magnis Dx NGS Prep System is designed for safe operation when it is used in the
intended manner. Using the system for purposes other than those intended may impair those
safety protections.
Installation
•The system must be installed by an Agilent engineer or Agilent authorized service provider.
•Do not attempt to manually lift the instrument. To move the instrument, use an automated
forklift or lift table that can lift at least 100 kg.
•When adjusting the placement of the instrument on the laboratory bench, take care to avoid
pinching hazards on the instrument.
•Retain the locking jigs that secure the gantry during shipment. Anytime the instrument is
moved, secure the gantry using the jigs.
Electrical
Standard electrical safety precautions should be applied, including the following:
•Per North American and IEC requirements, install the instrument in a location where branch
circuit protection is available in the power network.
•Install the instrument with the Agilent supplied power cord that is compatible with the
electrical outlets in your region. Do not substitute with a power cord from another source.
•Install the instrument in a location where the power cord can be easily reached for quick
disconnection of the power supply.
•Install the instrument away from any flammable sources.
•Make sure that the ventilation slots of the instrument are free to vent at all times. Maintain
10 cm of cleared space on each side of the instrument and 18 cm of cleared space at the back
of the instrument.
•Connect the power cord to a wall output that provides 100–240 VAC, 1000 W.
•Make sure that proper voltage is supplied before turning on the instrument for the first time.
•Connect the instrument to a grounded socket. Do not operate the instrument from a power
outlet that has no ground connection.
•Do not connect the instrument to the same circuit as other devices with a high current draw
(e.g., freezers, centrifuges). If possible, connect the instrument to an independent or dedicated
AC circuit.
•Do not touch any switches or outlets with wet hands.

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•Before disconnecting the power cord, turn off the instrument at both the power button on the
front and the power switch on the back.
•Unplug the instrument before you clean any major liquid spills and before servicing any of the
electrical or internal components.
•Do not operate the instrument in a hazardous or potentially explosive environment.
•Do not service the electrical components unless you are qualified to do so.
Fluids and Reagents
•Never process reagents not intended for use with the Magnis/Magnis Dx NGS Prep System.
•Observe the relevant safety regulations when handling pathogenic material, radioactive
substances or other substances hazardous to health.
•Do not submerge the instrument in any liquid.
Danger of Ultraviolet (UV) Light Exposure
The instrument door and side panels are not UV-transparent, therefore exposure to UV light is
minimal. However, the following precautions are still needed.
•During decontamination of the instrument deck with UV light, do not look directly or indirectly
at the UV light source.
•Always perform decontamination with the instrument door closed and locked. The instrument
door is programmed to remain locked while the UV light is on.
•Replacement UV tubes must be provided by Agilent and must be installed by an Agilent
engineer or Agilent authorized service provider.
Danger of Burns
•During protocol runs, the thermal block and other components of the thermal cycler module
quickly attain temperatures of greater than 50°C. To ensure safe operation, the instrument
door must remain closed during runs. The instrument door is programmed to remain locked
while protocol runs are in progress.
•Use only Agilent materials (plates, adhesive seals, foils, mats) intended for use on the
Magnis/Magnis Dx NGS Prep System. These materials are sufficiently temperature-stable (up
to 120°C).
Equipment Ratings
•Pollution degree 2
•Installation category II
•Altitude 2000 m
•Humidity 30 to 70%, non-condensing
•Electrical supply 100–240 V, 50/60 Hz, 1000 W
•Temperature 15°C to 25°C
•For Indoor Use Only

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Electrostatic Discharge
The Magnis/Magnis Dx NGS Prep System is static sensitive. Electrostatic discharges greater than
8000 volts may interfere with the normal operation of the USB ports on the instrument. Handling
precautions are required when working in high static environments. Wear a grounded wrist strap
and take other anti-static precautions prior to making contact with the instrument in high static
environments. ESD STM5.1-1998 Class 3B.
Environmental Requirements
Operating temperature
Keep the ambient temperature between 15°C and 25°C.
Operating humidity
Keep the humidity levels between 30% and 70% non-condensing.
Installation Requirements
•Place the instrument in a post-PCR laboratory environment.
•Do not place the instrument in proximity to other lab equipment that is sensitive to vibrations
or that generates vibrations during use.
•Maintain the following minimum distances for cleared space around the instrument.
•Instrument sides: 10 cm (4 inches) on each side to allow for proper ventilation from the side
vents.
•Back of the instrument: 18 cm (7 inches) at the back to allow for proper ventilation from the
back vent.
•Front of the instrument: 5 cm (2 inches) in front to avoid unintentional contact with the
power switch.
•Top of the instrument: 111 cm (44 inches) above to allow for opening the door.
•Install the instrument with the Agilent supplied power cord. Do not substitute with a power
cord from another source.
•Install the instrument in a location where the power cord can be easily reached for quick
disconnection of the power supply.
•Install the instrument away from any flammable sources.
Review the “Electrical” safety precautions on page 11 for power supply requirements that impact
safe operation of the instrument.
NOTE After installation is complete, avoid moving the instrument or making any
adjustments to the placement of the instrument as it may disturb some of the
settings made by the Agilent engineer or service provider.

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User Guide
14
2 Hardware Overview
Instrument Components 15
Instrument Status Indicator Lights 18
This chapter provides product information on the hardware elements of the Magnis/Magnis Dx
NGS Prep System.

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Instrument Components
The Magnis/Magnis Dx NGS Prep System includes the following instrument components.
Front and sides of instrument – Figure 1
•Instrument door
•Waste bin drawer containing disposable tip waste bin
•LCD touchscreen for display of the firmware software
•Power button
•USB ports (2)
•Side vents (1 on each side)
Figure 1 Instrument front, door closed
Instrument door
LCD touchscreen
USB ports
Waste bin drawer
Power button
Side vent

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Back of instrument – Figure 2
•Power switch
•Ethernet port
•Power cord inlet
•Back vent
Figure 2 Instrument back
Instrument interior – Figure 3 and Figure 4
•Instrument deck consisting of the following modules:
•Thermal cycler module for incubation and PCR steps
•Heater/shaker/magnet (HSM) module for various processing steps
•Chiller module for reagent storage
•Tube holders for liquid reagents (6 total)
•Platforms to hold tip boxes (4)
•Platform to hold Beads/Buffers Plate
•Opening to tip waste bin
•LED indicator lights (2)
•Micropipettor for liquid transfer
•Barcode scanner for labware verification and sample tracking
•Gantry for positioning of the micropipettor and barcode scanner
•UV tube for decontamination of surfaces of the instrument deck with UV light
Power switch
Ethernet port
Back vent
Power cord inlet

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Figure 3 Instrument interior
Figure 4 Instrument deck
Micropipettor
Barcode scanner
UV
tube
Instrument deck
LED indicator light
LED indicator light
Gantry
Tip box platforms
(3 loaded, 1 empty)
Chiller
(loaded)
Beads/Buffer Plate platform
(loaded)
HSM (loaded)
Thermal cycler (loaded)
Tube holders
(empty)
Tip waste
bin opening

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Instrument Status Indicator Lights
You can quickly and easily check the status of the instrument based on the color of the LED
indicator lights that illuminate the entire plate-filling area.
Table 5 Colors and descriptions of the LED indicator lights in the plate filling area
LED Color Instrument Status Description
White Ready The lights are illuminated white when the system is idle but the door is
open, when the system is performing auto-teaching or teach-point
verification, and when a user is setting up a protocol run.
Blue Ready The lights are illuminated blue anytime the system is idle and the door
is closed, including at completion of a protocol run. The lights are also
blue when the system is performing diagnostic tests.
Green Running The lights are illuminated green when the system is running a protocol.
Red Error The lights are illuminated red when the system has encountered an
error. Check the touchscreen for an error message containing further
details.
WARNING During UV decontamination, the indicator lights are off and the
instrument deck is illuminated by the UV light. Do not look directly at the
UV light.

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User Guide
19
3 Getting Started
Starting Up the Magnis/Magnis Dx NGS Prep System 20
Turn on the instrument 20
Log in to the system 20
Managing User Accounts 22
About user access levels 22
Add new user accounts 22
Edit user accounts 24
Disable user accounts 25
Programming System Settings 27
Set the chiller temperature 27
Set the time and date 27
Assign an instrument name 28
View the instrument serial number and software version 29
Set up the instrument IP address 29
Set the instrument health check settings 30
Setting Up Email Alerts and Protocol Alerts 32
Set up the email settings for outgoing email alerts 32
Set up alerts for notification of new protocols 33
This chapter contains instructions for logging in to the software, setting up and editing user
accounts, configuring system settings, and setting up email notifications.

Magnis and Magnis Dx NGS Prep System User Guide 20
Starting Up the Magnis/Magnis Dx NGS Prep System
Turn on the instrument
The power button on the front of the instrument is to toggle the instrument on and off.
1Press the power button on the front of the instrument.
The light on the power button turns green, the instrument turns on, the LED indicator lights
inside the instrument illuminate, and the software launches on the touchscreen.
If pressing the power button fails to turn on the instrument, verify that the power switch on the
back of the instrument is in the ON position.
Log in to the system
If you do not yet have your own personal user account, use the user name and password provided
by the Agilent engineer or service provider who installed your system.
1Access the Login screen of the software.
The Login screen opens automatically after turning on the instrument.
If another user is already logged in, press the user name at the bottom of the screen then press
Log Out. The previously logged in user is logged out and the Login screen opens.
Figure 5 Login screen
2Type the user name and password for your account into the provided fields.
The Agilent engineer or Agilent authorized service provider creates a user account during
system installation that has advanced user access.
3Press Login.
You are now logged in to the software.
Stand by as the system performs the series of preparatory activities described in Table 6. At
the end of the preparatory activities, the software opens to the Home screen.