Agilent Technologies Magnis NGS Prep System User manual

Before You Begin 2
Safety Precautions 2
Environmental Requirements 4
Instrument Components 4
Starting Up the Magnis NGS Prep System 7
Turn on the instrument 7
Log in to the system 7
Creating User Accounts 8
About user access levels 8
Add new user accounts 9
Decontaminating the System 9
Running Protocols 10
1) System prep 10
2) Reagent prep 11
3) Protocol set up and run 11
4) Collection and clean up 12
Magnis NGS Prep System, G9710AA
Quick Reference Guide
For Research Use Only. Not for use in diagnostic procedures.

Before You Begin
2 Magnis NGS Prep System Quick Reference Guide
Before You Begin
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.
Principle of the
Procedure
The Agilent Magnis 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 4 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.
Limitations of
Use
The Magnis NGS Prep System has been validated for use with Agilent Magnis NGS kits.
Materials
Provided
Safety Precautions
The Magnis 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.
Table 1 Materials provided with the Magnis NGS Prep System
Materials
Magnis NGS Prep System instrument and preloaded touchscreen software
Power cord
Functional test certificate
USB disk with PDFs of the User Guide and Quick Reference Guide

Safety Precautions
Magnis NGS Prep System Quick Reference Guide 3
•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.
•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 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
Although exposure to UV light is minimal, 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. Keep the instrument door 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
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

Environmental Requirements
4 Magnis NGS Prep System Quick Reference Guide
Electrostatic
Discharge
The Magnis 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.
Instrument Components
Front and sides
of instrument
•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
Back of
instrument
•Power switch
•Ethernet port
•Inlet for power cord
Instrument door
LCD touchscreen
USB ports
Waste bin drawer
Power button
Side vent

Instrument Components
Magnis NGS Prep System Quick Reference Guide 5
•Back vent
Figure 2 Instrument back
Instrument
interior
•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

Instrument Components
6 Magnis NGS Prep System Quick Reference Guide
Figure 3 Instrument interior
Figure 4 Instrument deck
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.
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

Starting Up the Magnis NGS Prep System
Magnis NGS Prep System Quick Reference Guide 7
Starting Up the Magnis 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 the 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.
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 3.
Table 2 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.

Creating User Accounts
8 Magnis NGS Prep System Quick Reference Guide
Creating User Accounts
About user
access levels
The access level assigned to a user account – Standard or Advanced – determines the user’s
access to certain software settings and functions. The table below summarizes the differences in
privileges between the two access levels.
Table 3 Preparatory steps
Step Description
Hardware initialization During hardware initialization, the system returns all motorized parts (i.e.,
the gantry, HSM module, and thermal cycler) back to their home positions.
Additionally, the system checks for the presence of any tips on the
micropipettor and, if necessary, disposes of those tips in the tip waste bin.
Instrument Health Check
(IHC)
The system performs an IHC each time it is powered on (after login) and
each time a protocol run is initiated. The checks performed during the IHC
ensure that the hardware is functioning within specifications.
Teach-point verification Auto-teaching is a process in which the system locates and records the
positions of markers (called teach points) that are printed on the
instrument deck. Auto-teaching ensures that, during a run, the
micropipettor is accurately aligned with the tubes or wells at each deck
position.
You can configure the system settings to include teach-point verification
as part of the initial IHC that is performed after powering up the
instrument. During teach-point verification, the current teach-point
locations are compared to those that were previously recorded during the
most recent auto-teaching run to ensure that the values are sufficiently
within range of each other. If the values do not fall within the expected
range, the system prompts you to rerun auto-teaching.
Table 4 Actions permitted for Standard and Advanced user account
Action Permitted by
Standard users?
Permitted by
Advanced users?
Set up and run protocols Yes Yes
View data from their own protocol runs Yes Yes
View data from protocol runs of other users No Yes
Update the number of PCR cycles during run setup No Yes
Edit user accounts of other users No Yes
Edit chiller temperature setting No Yes
Install firmware and protocol updates No Yes
Edit protocol and email alert settings No Yes
Delete diagnostic reports No Yes
Change default protocol version No Yes

Decontaminating the System
Magnis NGS Prep System Quick Reference Guide 9
Add new user
accounts
Each user who uses the system needs an account.
1From the Home screen, press Settings.
2Press User Management.
The User Management screen opens listing the available user names and corresponding
access levels and statuses.
3Press Add.
The Add New User screen opens.
4In the User Name field, enter a user name for the new account.
User names can contain a combination of letters and numbers, but numbers are only
permitted at the end of the user name (e.g., abc123). Do not include special characters in the
user name.
5Next to Access Level, select the access level (Standard or Advanced) for the new user. The
default selection is Standard.
See Table 4 for a summary of the differences between the two access levels.
6In the Password and Confirm Password fields, enter a password for the account.
7In the Email address(es) field, enter one or more email addresses to associate with the user
account.
Separate multiple email addresses with a space. You can enter up to five email addresses.
When the system needs to send an email alert to the user, it sends it to all email addresses
listed in the Email address(es) field.
8Mark the check box labeled Email alert on run complete if you want the system to send an
email alert to the user when it completes a protocol that was initiated by that user.
9Mark the check box labeled Email alert on error occurs if you want the system to send an
email alert to the user when it encounters an error during a protocol run that was initiated by
that user.
10 Press OK to save the user account.
The Add New User screen closes and you are returned to the User Management screen. The
new user name appears in the list on the User Management screen.
Decontaminating the System
The Magnis NGS Prep System includes a UV tube that can be used to decontaminate the surfaces
of the instrument deck. The quick cycle is a 30-minute decontamination. Agilent recommends
running the quick cycle before each protocol run. The 2-hour extended cycle is recommended in
the event of a spill or leak on the deck surfaces.
Instructions for running a quick cycle are provided below. For instructions on running an extended
cycle, see the full-length Magnis NGS Prep System User Guide (publication K1007-90000).
WARNING Do not look directly at the UV light while decontamination is in progress.

Running Protocols
10 Magnis NGS Prep System Quick Reference Guide
Run a quick
cycle
Agilent recommends running the decontamination quick cycle before each protocol run.
1Verify that the instrument deck is cleared of all labware, then make sure that the instrument
door is closed.
2From the Home screen, press Decontamination.
The Decontamination screen opens.
Figure 5 Decontamination screen with Quick cycle selected
3At the top of the screen, select Quick cycle, as shown in Figure 5
4Press Start.
The decontamination cycle begins and the screen displays a countdown of the time remaining.
At the completion of the cycle, the UV light turns off and the instrument remains idle.
If needed, press Abort at any time to stop the decontamination cycle.
Running Protocols
1) System prep Prepare the Magnis NGS Prep System so that it is ready to run a protocol.
1Verify that the instrument deck is cleared of all labware from previous runs.
2Turn on the instrument and close the instrument door.
See “Turn on the instrument” on page 7 for instructions.
3At the Login screen, enter the credentials for your user account.
Each time the system is turned on, it performs a series of start up activities (see Table 3 on
page 8) immediately after login. These activities may take several minutes to perform. Make
sure the instrument door remains closed for the duration of these activities. After completion
of the start up activities, the software opens to the Home screen and the system’s LED light is
blue, indicating that it is ready for use.
4(Optional) Perform the 30-minute UV decontamination quick cycle to decontaminate the
surfaces of the instrument deck. See “Decontaminating the System” on page 9.
You can begin “2) Reagent prep” while the decontamination is running.

Running Protocols
Magnis NGS Prep System Quick Reference Guide 11
For instructions on manually decontaminating the surfaces of the instrument deck, consult the
full-length Magnis NGS Prep System User Guide (publication K1007-90000).
2) Reagent prep Prepare the samples, target enrichment reagents, and other materials needed for the protocol run
according to the user manual for your specific Magnis Target Enrichment Kit. The user manual
contains details on the materials required to run a protocol and instructions on loading your DNA
samples into the Magnis Sample Input Strip.
The image below describes the orientation of the Magnis Sample Input Strips. Make sure to track
the locations of your samples as you load them into the strip.
Figure 6 Orientation of the Magnis Sample Input Strips
3) Protocol set
up and run
For detailed instructions on running a protocol for your particular sample type, refer to the user
manual for your Magnis Target Enrichment Kit.
1From the Home screen, press Run Protocol.
The system locks the instrument door and performs an IHC. At completion of the IHC, the
Enter Run Info step opens.
2Complete the Run Setup steps and start the protocol run, as instructed in the user manual for
your Magnis Target Enrichment Kit.
The software walks you through the individual Run Setup steps (Figure 7), starting with the
Enter Run Info step. Press the forward and back arrow buttons to navigate through the steps
(or, if using a USB-connected mouse, click the arrow buttons with the cursor). Because the
steps vary depending on the type or target enrichment you are running, you will need to refer to
the instructions and screen images provided in the user manual for your Magnis Target
Enrichment Kit.
After you start the run, the system’s LED light turns green, indicating that a protocol run is in
progress. The LED changes from green to blue upon completion of a the run. Additionally, if your
account is set up to receive email alerts, the system sends you an email when the run is complete.
If the system encounters an error during the protocol, the LED light changes to red and, if your
account is configured for alerts, the system sends you an email notifying you of the error.
CAUTION Do not add any writing or labels to the strips, plates, and other labware that
may obscure the barcodes.

Running Protocols
12 Magnis NGS Prep System Quick Reference Guide
Figure 7 Protocol workflow, with corresponding color of LED status indicators lights
4) Collection
and clean up
At the completion of the run, the system keeps the prepared library solutions in the PCR plate on
the thermal cycler module, which is held at 12°C for up to 72 hours. Collect the samples within
that 72-hour period.
1Wait until the touchscreen indicates that the run is complete. Press OK when you are ready to
collect the library samples from the instrument.
The system transfers the libraries from the PCR plate to the green library strip tube in the
chiller. Allow the instrument-mediated transfer process to complete before continuing.
2At the completion of the transfer process, open the instrument door and collect the final library
samples (i.e., the green library strip tube) from the chiller module.
3Re-seal the wells of the strip tube using a fresh foil seal strip, then store at the temperature
recommended in the user manual for your Magnis Target Enrichment Kit.
4If the optional pre-capture library QC samples were collected for the run, remove the blue QC
sample strip from the chiller module. Process and store the samples as recommended in the
user manual for your Magnis Target Enrichment Kit.
5Remove all remaining consumables from the instrument deck and dispose of them according
to local guidelines. Close the instrument door.
6Log out of the software or turn off the instrument.
To log out, press the user name at the bottom of the screen then press Log Out.
To turn off the instrument, press the power button on the front of the instrument.
Run Setup Steps
Enter Run Info
Set Up Deck
Verify Labware
Enter Sample Info
Confirm Setup & Start Run
LED: white
Running
Complete
LED: green
LED: blue

Revision A0, June 2019
*G9710-90000*
G9710-90000
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