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.

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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