Thermo Scientific Ion Torrent Genexus Integrated Sequencer User manual

For Research Use Only. Not for use in diagnostic procedures.
Genexus™Integrated Sequencer
USER GUIDE
Catalog Number A45727
Publication Number MAN0017910
Revision A.0

Manufacturer:
Life Technologies Holdings Pte Ltd |
Block 33 |
Marsiling Industrial Estate Road 3 |
#07-06, Singapore 739256
Products:
Genexus™Integrated Sequencer
Genexus™Software
Manufacturer:
Life Technologies Corporation |
7335 Executive Way |
Frederick, MD 21704 | USA
Products:
GX5™Chip and Genexus™Coupler
Genexus™Library Strips 1 and 2‑AS
Genexus™Library Strips 1 and 2‑HD
Genexus™Templating Strips 3 and 4‑GX5™
Genexus™Barcodes 1–96 AS
Genexus™Barcodes 1–32 HD
Genexus™Primer Pool Tubes
Genexus™Pipette Tips
Genexus™Sequencing Kit
Genexus™Controls
Genexus™GX5™Starter Pack‑AS
Genexus™GX5™Starter Pack‑HD
Oncomine™GX assays
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL,
INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,
INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0017910
Revision Date Description
A.0 13 November 2019 New user guide for the Genexus™Integrated Sequencer
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept
the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Microsoft and Excel are
trademarks of Microsoft Corp. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license.
©2019 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ....................................... 8
Product description ............................................................. 8
Genexus™Integrated Sequencer .................................................. 9
Reagents and supplies—Ion AmpliSeq™library chemistry ........................... 10
Genexus™Library Strips 1 and 2‑AS .......................................... 10
Genexus™Barcodes AS ..................................................... 10
Genexus™GX5™Starter Pack‑AS ............................................. 11
Reagents and supplies—Ion AmpliSeq™HD library chemistry ....................... 12
Genexus™Library Strips 1 and 2‑HD .......................................... 12
Genexus™Barcodes 1–32 HD ................................................ 12
Genexus™GX5™Starter Pack‑HD ............................................ 13
Shared reagents and supplies ................................................... 14
Genexus™Templating Strips 3 and 4‑GX5™.................................... 14
Genexus™Primer Pool Tubes and Pipette Tips ................................. 14
GX5™Chip and Genexus™Coupler ............................................ 15
Genexus™Sequencing Kit ................................................... 15
Genexus™Controls ......................................................... 16
Genexus™Filter ........................................................... 16
Oncomine™GX assays .......................................................... 16
Required materials not supplied ................................................. 17
Recommended materials for nucleic acid isolation and quantification ................. 18
Genexus™Integrated Sequencer components ...................................... 19
Genexus™Integrated Sequencer deck stations ..................................... 20
Genexus™Integrated Sequencer input and output connections ....................... 21
Workflow ..................................................................... 22
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■CHAPTER 2 Before you begin .......................................... 23
Precautions ................................................................... 23
Avoid nucleic acid contamination ............................................. 23
Avoid chip damage ......................................................... 23
Avoid strong electromagnetic radiation ....................................... 23
Protection by equipment .................................................... 23
Guidelines for Genexus™Integrated Sequencer operation ........................... 24
Power the Genexus™Integrated Sequencer on or off ............................... 25
Power on ................................................................. 25
Power off ................................................................. 26
Get started with Genexus™Software .............................................. 26
About the Genexus™Software user interface .................................. 26
User-access levels ......................................................... 27
System tracking ........................................................... 27
Request and sign in to a new account ......................................... 27
Sign in .................................................................... 28
■CHAPTER 3 Create and manage
assays (manager/administrator) ........................................ 29
About assays in Genexus™Software .............................................. 29
System-installed assays ........................................................ 30
Manage assays (manager/administrator) ......................................... 30
Create a new assay (manager/administrator) ...................................... 32
Copy an assay (manager/administrator) .......................................... 40
Import an assay (manager/administrator) ......................................... 41
■CHAPTER 4 Enter samples and libraries ............................. 42
Add a new sample .............................................................. 42
System-installed sample attributes .......................................... 43
Create a custom sample attribute (manager/administrator) ..................... 44
Import samples ............................................................... 45
Manage samples ............................................................... 46
Sort, search, and filter samples ............................................. 46
Export and print samples ................................................... 47
View notes or add a note to a sample ......................................... 48
Edit a sample (manager/administrator) ...................................... 48
Edit a sample and amend a report after a run (manager/administrator) .......... 49
Review sample edit history .................................................. 49
Delete samples ............................................................ 50
Prepare or import a library batch ................................................ 50
Prepare a library batch ..................................................... 50
Import a library batch ...................................................... 53
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■CHAPTER 5 Create and manage run plans .......................... 55
Create a run plan for a sample run ............................................... 56
Create a run plan for a library run ................................................ 63
■CHAPTER 6 Dilute the samples and load the sample plate ......... 68
Guidelines for nucleic acid isolation and quantification—sample runs ................. 68
Dilute the samples (if needed) and load the sample plate—sample run ............... 69
Guidelines for library quantification—library runs .................................. 71
Dilute and pool libraries, and load the sample plate—library run ..................... 71
■CHAPTER 7 Load the sequencer and start a run ..................... 72
Before you begin ............................................................... 72
Fill Genexus™Primer Pool Tubes
(custom assays only) ............................. 74
Load the sequencer and start a run ............................................... 75
Clear the instrument deck and perform a UV Clean ................................. 81
■CHAPTER 8 Monitor the run ........................................... 84
View run progress on the instrument ............................................. 84
■CHAPTER 9 Review data and results .................................. 85
Run Results screen ............................................................ 86
Lab Report .................................................................... 88
Download the Lab Report ................................................... 89
View sequencing results and run metrics ......................................... 89
Summary of the sample results ............................................. 91
Run metrics ............................................................... 92
QC results ................................................................ 94
SNV/INDEL results ......................................................... 95
Fusion results ............................................................. 97
CNV results ............................................................... 99
View annotation sources ................................................... 101
Create and assign variant classifications ..................................... 102
Filter results ............................................................. 102
View Oncomine™TCR Beta‑LR Assay GX run results ........................... 105
Sign off on the run results (manager/administrator) .............................. 107
Generate customized reports ................................................... 108
Results files .................................................................. 109
Review coverageAnalysis plugin results .......................................... 111
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Upload sample results files to Ion Reporter™Software ............................. 111
Verification runs .............................................................. 113
View and sign off on the verification run results (Field Service Engineer) ........ 114
■APPENDIX A Troubleshooting ........................................ 117
Genexus™Software ........................................................... 117
Genexus™Integrated Sequencer ................................................ 119
■APPENDIX B Touchscreen reference ................................ 120
Touchscreen icons ............................................................ 120
Settings ..................................................................... 121
Network Settings ......................................................... 122
Perform a Clean instrument operation ...................................... 124
System Tools ............................................................. 124
Data Management ........................................................ 129
Instrument settings ....................................................... 131
■APPENDIX C Supplemental information ............................ 134
Maintain the sequencer ........................................................ 134
Materials required ........................................................ 134
Clean or decontaminate the sequencer ...................................... 134
Replace the Genexus™Filter ............................................... 135
Quantify FFPE DNA with the Qubit™Fluorometer .................................. 135
Guidelines for using custom assays with the Genexus™Integrated Sequencer ........ 136
Planning sequencing runs for efficient use of consumables ........................ 138
Configure an Ion Reporter™Server account (administrator) ........................ 139
Tag an Ion Reporter™Software analysis workflow for use with the
IonReporterUploader plugin ............................................... 140
Configure Thermo Fisher (Connect) accounts (manager/administrator) .............. 141
■APPENDIX D coverageAnalysis plugin in Genexus™Software .... 143
Reads statistics .............................................................. 143
Example Coverage Analysis Report .............................................. 145
Example charts generated by the coverageAnalysis plugin ......................... 147
Output files generated by the coverageAnalysis plugin ............................. 148
■APPENDIX E Safety .................................................... 150
Symbols on this instrument .................................................... 150
Standard safety symbols ................................................... 150
Additional safety symbols .................................................. 152
Location of safety labels ................................................... 152
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Control and connection symbols ............................................ 153
Conformity symbols ....................................................... 153
Instrument safety ............................................................. 154
General ................................................................. 154
Physical injury ........................................................... 154
Electrical safety .......................................................... 155
Cleaning and decontamination ............................................. 156
Instrument component and accessory disposal ............................... 156
Safety and electromagnetic compatibility (EMC) standards ......................... 156
Safety standards .......................................................... 157
EMC standards ........................................................... 157
Environmental design standards ............................................ 158
Radio compliance standards ............................................... 158
Chemical safety ............................................................... 159
Biological hazard safety ........................................................ 161
■APPENDIX F Documentation and support .......................... 162
Related documentation ........................................................ 162
Customer and technical support ................................................ 162
Limited product warranty ...................................................... 162
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Product information
■Product description .................................................... 8
■Genexus™ Integrated Sequencer ......................................... 9
■Reagents and supplies—Ion AmpliSeq™ library chemistry ................. 10
■Reagents and supplies—Ion AmpliSeq™ HD library chemistry ............. 12
■Shared reagents and supplies .......................................... 14
■Oncomine™ GX assays ................................................ 16
■Required materials not supplied ........................................ 17
■Recommended materials for nucleic acid isolation and quantication ....... 18
■Genexus™ Integrated Sequencer components ............................ 19
■Genexus™ Integrated Sequencer deck stations ............................ 20
■Genexus™ Integrated Sequencer input and output connections ............. 21
■Workow ........................................................... 22
Product description
The Ion Torrent™ Genexus™ Integrated Sequencer is a next-generation high-
throughput sequencing system that integrates library preparation, templating, and
sequencing into a single-day, single-instrument automated run. The instrument
supports both sample-to-results and library-to-results sequencing runs (up to 32 DNA
or RNA samples/run). Additional key features include:
• Sample to results in as lile as 14 hours (single lane run)
• Flexible and cost-eective run planning making use of multi-lane, multi-run
sequencing chips
• Automated library preparation for up to 400 base-read libraries using either
standard Ion AmpliSeq™ or Ion AmpliSeq™ HD library chemistry
• Automated Ion Sphere™ Particle (ISP)-loading and templating with on-chip
amplication
• Support for up to four compatible assays on a GX5™ Chip in a single run
• As lile as ve minutes total hands-on time required per run
• Real-time consumables tracking by the instrument to guide consumable loading
during run setup
• Consumables that are usable for up to 14 days after loading
• On-instrument sequencing data analysis requiring no external server
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Genexus™Integrated Sequencer
The Genexus™ Integrated Sequencer includes the following components.
Components Cat. No.
Genexus™Integrated Sequencer A45727
Genexus™Installation and Training Kit A40278[1]
[1] Not available for separate purchase.
The Ion Torrent™ Genexus™ Installation and Training Kit (Cat. No. A40278) is
available to rst-time owners of a Genexus™ Integrated Sequencer and is shipped with
the instrument. The kit contains the following reagents, supplies, and controls that are
used during the installation, training, and operation of the instrument.
Genexus™Installation and Training Kit
Contents Part No. Quantity Storage
Genexus™Controls A40267 1 −30°C to −10°C
Genexus™Strip 1 A40254 8 strips 2°C to 8°C
Genexus™Strip 2‑AS A40253 8 strips −30°C to −10°C
Genexus™Barcodes 1–32 AS A40258 1 plate 15°C to 30°C
Genexus™Strip 3‑GX5™A40265 8 strips 2°C to 8°C
Genexus™Strip 4 A40264 8 strips −30°C to −10°C
Genexus™Cartridge A40272 2 cartridges −30°C to −10°C
Genexus™Bottle 2 A40273 4 bottles
15°C to 30°C
Genexus™Bottles 1 and 3 A40274 2 bottles each
Genexus™Pipette Tips A40266 12 racks
Genexus™Conical Bottles A40275 2 sets of 5 bottles
Genexus™Filter A40302 1
Chapter 1 Product information
Genexus
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Integrated Sequencer
1
Genexus
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Integrated Sequencer User Guide
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Reagents and supplies—Ion AmpliSeq™library chemistry
Genexus™ Integrated Sequencer reagents and supplies can be ordered in convenient
combo kits and starter packs, but most consumables can also be ordered individually
as your needs require. The following tables provide information on the various
ordering options that are available for Ion AmpliSeq™ library chemistry.
Note:
·Consumables that have catalog numbers are orderable. Components that have part
numbers cannot be ordered individually.
·Reagents that are specic to Ion AmpliSeq™ library chemistry have an AS sux.
Ion Torrent™ Genexus™ Library Strips 1 and 2-AS (Cat. No. A40252) for standard Ion
AmpliSeq™ library-based chemistry are ordered as kits with eight pairs of strips/kit.
Component Carrier color Part No. Quantity per
kit Storage
Genexus™Strip 1 Red A40254 8 strips 2°C to 8°C
Genexus™Strip 2‑AS Blue A40253 8 strips −30°C to
−10°C
Ion Torrent™ Genexus™ Barcodes AS are supplied in plates containing 32 dual
barcodes per plate. The barcodes can be ordered as a set of three plates (Cat. No.
A40257), or ordered individually.
Item Label color Cat. No. Quantity Storage
Genexus™Barcodes 1–96 AS Blue A40257 3 plates 15°C to 30°C
Genexus™Barcodes 1–32 AS Blue A40258 1 plate
Genexus™Barcodes 33–64 AS Blue A40259 1 plate
Genexus™Barcodes 65–96 AS Blue A40260 1 plate
Genexus™Library
Strips 1 and 2‑AS
Genexus™
Barcodes AS
Chapter 1 Product information
Reagents and supplies—Ion AmpliSeq
™
library chemistry
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Integrated Sequencer User Guide