Agilent Technologies Magnis G9710A User manual

Magnis/MagnisDx NGS Prep System
User Guide
K1007A MagnisDx NGS Prep system: For In Vitro Diagnostic Use
G9710A Magnis NGS Prep system: For Research Use Only. Not for use in diagnostic procedures.
Revision C0, May 2022

Magnis and MagnisDx 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. 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
UK Responsible Person Unique Device Identifier
UK Conformity Assessed Regulatory Compliance mark
KC EMC
WARNING

Magnis and MagnisDx NGS Prep System User Guide 3
South Korean Class A EMC Declaration
This equipment has been evaluated for its suitability for use in a commercial environment. When
used in a domestic environment, there is a risk of radio interference.
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Magnis and MagnisDx NGS Prep System User Guide 4
Content
1 Before You Begin 8
Product Description 9
Intended Use 9
Principle of the NGS Prep Procedure 9
Limitations of Use 9
Instrument Specifications 10
Materials Provided 11
Optional USB Disk 11
Cleaning Supplies 11
Product Inspection 12
Safety Precautions 12
Environmental Requirements 14
Installation Requirements 14
2 Hardware Overview 15
Instrument Components 16
Instrument Status Indicator Lights 19
3 Getting Started 20
Starting Up the Magnis/MagnisDx NGS Prep System 21
Turn on the instrument 21
Log in to the system 21
Managing User Accounts 23
About user access levels 23
Add new user accounts 23
Edit user accounts 25
Disable user accounts 26
Programming System Settings 28
Set the chiller temperature 28
Set the time and date 28
Assign an instrument name 29
View the instrument serial number and software version 30
Set up the instrument IP address 30
Set the instrument health check settings 31
Setting Up Email Alerts and Protocol Alerts 33
Set up the email settings for outgoing email alerts 33
Set up alerts for notification of new protocols 34

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4 Operating the System 35
Running Protocols 36
Prepare the instrument for running a protocol 36
Prepare the reagents and plasticware 36
Set up and initiate the protocol run 37
Collect final library samples and clean up the system 38
Running and Viewing Diagnostic Tests 39
Perform instrument diagnostic tests 39
View reports for diagnostic tests and instrument health checks 40
Decontaminating with UV Light 42
Run a decontamination “quick cycle” 42
Run a UV decontamination “extended cycle” 43
Running Auto-Teaching and Teach-Point Verification 44
Run auto-teaching 44
Include teach-point verification in the IHC 45
Installing Updates 46
Install protocol updates 46
Install firmware updates 48
5 Performing Maintenance 50
Annual Preventative Maintenance 51
Cleaning the System Components 52
Precautions to take when cleaning the system components 52
Clean the deck surfaces and instrument exterior 52
Clean the barcode scanner 55
Replacing the UV Tube and Viewing UV Tube Usage 56
Request a UV tube replacement 56
View usage hours for the UV tube 56
Disposing of Instrument Parts 57
6 Software User Interface Reference 58
Software User Interface Overview 59
Login screen 61
Home screen 62
Settings screens 63
Settings screen 63
User Management screen 64
Add New User screen 65

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Edit User screen 66
System Settings screen 67
Export Files screen 68
Protocols screen 69
Protocol Update screen 70
Connectivity Settings screen 71
Auto Teach screen 72
Hardware Usage Tracking screen 73
Instrument Diagnostic screen 73
System Settings screens 75
Instrument Settings screen 75
Date & Time Settings screen 76
Chiller Setting screen 77
Firmware Update screen 77
Connection Settings screen 78
Other Settings screen 79
Instrument Diagnostic screens 81
Diagnostic Test screen 81
Diagnostic Test Report screen 82
Diagnostic Report Explorer screen 83
Decontamination screen 84
Run Data Explorer screen 85
Post Run Data screen 86
Run Setup tab 86
Run Info tab 87
Labware Info tab 87
Audit Trails tab 88
Protocol Wizard screens 89
Connectivity Settings screens 90
Email Alert Settings screen 90
Protocol Alert Settings screen 91
Run screens 92
Run screen when run is in-progress 92
Run screen when run is complete 93
Run screen when sample collection is in-progress 93
Run screen when libraries are ready 94
7 Troubleshooting 96
Troubleshooting Suggestions 97

Magnis and MagnisDx NGS Prep System User Guide 7
Magnis system issues 97
Library/sequencing issues 98

Magnis/MagnisDx NGS Prep System
User Guide
8
1 Before You Begin
Product Description 9
Intended Use 9
Principle of the NGS Prep Procedure 9
Limitations of Use 9
Instrument Specifications 10
Materials Provided 11
Optional USB Disk 11
Cleaning Supplies 11
Product Inspection 12
Safety Precautions 12
Environmental Requirements 14
Installation Requirements 14
This chapter contains information for you to read and understand before you start.

Magnis and MagnisDx NGS Prep System User Guide 9
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 MagnisDx 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 MagnisDx 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/MagnisDx 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 16
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/MagnisDx
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/MagnisDx NGS Prep System has been validated for use with Agilent Magnis NGS
kits.

Magnis and MagnisDx NGS Prep System User Guide 10
Instrument Specifications
* The listed conditions apply to instrument operation. Conditions required for assay performance may
differ.
‡The maximum length of the LAN cable used for EMC testing is 1.5 meters.
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 ± 10%
AC frequency 50/60 Hz
Maximum power 1000 W
Input/output (I/O) connectors
USB 2.0 port Maximum voltage rating 5 VDC
LAN port (for Cat
5 cable‡)
Maximum voltage rating 3.3 VDC
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