For Research Use Only. Not for use in diagnostic procedures.
Oncomine™ Focus Assay, Part III: Plan a Run
USER GUIDE
Publication Number MAN0013551
Revision D.0
The information in this guide is subject to change without notice.
DISCLAIMER
TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES 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
Table 1 Revision history of MAN0013551
Revision Date Description
D.0 3 February 2016 Updated the Oncomine™ Focus Assay
documentation set with information about Torrent
Suite™ Assay Development Software
C.0 16 October 2015 Minor user interface name changes in Torrent
Suite™ Software v5.0.
B.0 10 July 2015 Designed BED file name change
A.0 27 May 2015 New document
Important Licensing Information
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applicable Limited Use Label Licenses.
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TRADEMARKS
All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
©2016 Thermo Fisher Scientific Inc. All rights reserved.
Contents
■CHAPTER 1 Create a Planned Run ..................................... 4
Create a Planned Run in Torrent Suite™ Software .................................... 4
Planned Run templates ...................................................... 4
Create a DNA and Fusions Planned Run ....................................... 5
Create and execute a Planned Run in Torrent Suite™ Assay Development Software ..... 10
Importing data into an Ion Reporter™ server ................................... 12
■APPENDIX A Make Oncomine™ Focus Assay templates
available in Torrent Suite™ Software .................................... 13
■APPENDIX B Sample Uploading Tips in Torrent Suite™ Software .. 16
Create sample sets manually .................................................... 16
Import samples to create Sample Set ............................................. 17
Create a planned run with sample set ............................................ 18
Create a planned run for mixed sample set ........................................ 19
Create a planned run for mixed samples by template ............................... 21
■APPENDIX C Create an RNA Fusions Planned Run in Torrent
Suite™ Software ........................................................... 23
Create a planned Oncomine™ Focus RNA Fusions run ............................... 23
■APPENDIX D Documentation and support ............................ 28
Related documentation ......................................................... 28
Customer and technical support ................................................. 28
Limited product warranty ....................................................... 29
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
3
Create a Planned Run
This chapter describes how to create Planned Runs in the following software
programs for use on the following systems.[1]
Software Instrument System
Torrent Suite™ Software, version 5.0 or later Ion PGM™ System
Torrent Suite™ Assay Development Software,
version 5.0 or later
Ion PGM™ Dx System
Create a Planned Run in Torrent Suite™ Software
This section provides a summary of steps for creating a Planned Run in Torrent Suite™
Software, for use on the Ion PGM™ System.
For more detailed instructions, see the Torrent Suite™ Software User Interface Guide,
available on the Ion Community.
In Torrent Suite™ Software, the primary Planned Run template to be used with the
Oncomine™ Focus Assay is the Oncomine™ Focus DNA and Fusions template. The
Oncomine™ Focus DNA and Oncomine™ Focus Fusion templates can be used when
you do not have sample pairs.
Note: Oncomine™ Planned Run templates are automatically installed with Torrent
Suite™ Software, but must be enabled in the software before use. See Appendix A,
1
Planned Run
templates
[1] The Ion PGM™ Dx System with Torrent Suite™ Assay Development Software is For Research
Use Only. Not for use in diagnostic procedures.
4
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
“Make Oncomine™ Focus Assay templates available in Torrent Suite™ Software“ for
instructions on enabling the template.
Template category Template name in Torrent
Suite™ Software Description
DNA and Fusions Oncomine™ Focus DNA and
Fusions
DNA and RNA planned run
template
Ion AmpliSeq™ DNA Oncomine™ Focus DNA DNA-only planned run
template
DNA and Fusions Oncomine™ Focus Fusions RNA-only planned run
template
1. Log into Torrent Suite™ Software.
2. Click the Plan tab, then click Templates.
3. Select DNA and Fusions from the list in the left panel.
The Oncomine™ Focus DNA and Fusions template appears in the Template
Name column. (If it does not appear, see Appendix A, “Make Oncomine™ Focus
Assay templates available in Torrent Suite™ Software“ to enable Oncomine™
templates.) For more information about creating Planned Runs manually or from
templates, see the Torrent Suite User Guide available on the Help>Local
documentation menu in Torrent Browser software.
4. If you have already created a template from the factory workow, proceed to
step 7. If you have not, please follow the optional steps below to create your
template.
5. (Optional) Create a copy of the Oncomine™ DNA and Fusions template to use the
same parameters for every planned run.
a. Click gear buon to access the Copy function.
6. (Optional) Dene your template on the Copy Template page.
a. Enter a new name for the template.
Create a DNA and
Fusions Planned
Run
Chapter 1 Create a Planned Run
Create a Planned Run in Torrent Suite™ Software
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Oncomine™ Focus Assay, Part III: Plan a Run User Guide
5
b. Verify the DNA Reference Library.
c. Add DNA Target Regions BED le. This le can be obtained through eld
support personnel. Install from USB key or download from email.
d. Enter a note about the template (if desired).
e. Click Copy Template.
Your new template appears under the Template Name column.
7. In the Template Name column, click on the template to create a run from that
template.
The wizard opens on the Plan tab.
8. Verify DNA Target Regions BED le that you added in step 6c and then proceed
to the next chevron.
Note: DNA Hotspot Regions, RNA Reference Library, or RNA Target Regions
are not necessary for analysis in Torrent Suite™ and Ion Reporter™ software
applications and can be left blank.
9. Click on the Ion Reporter™ chevron, then select the Ion Reporter™ version 5.0
account. If the version 5.0 account is not congured, congure it through Ion
Reporter Congure seings. See Congure the Uploader plugin in the Torrent
Browser topic in Torrent Suite™ Software Help for details.
a. Select the Oncomine™ Focus v2.0 - DNA and Fusions - Single Sample
workow from the Existing Workow drop-down menu.
Chapter 1 Create a Planned Run
Create a Planned Run in Torrent Suite™ Software
1
6
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
b. Click Next.
10. On the Application page, verify that the appropriate application and target
technique are pre-selected. Click Next.
Chapter 1 Create a Planned Run
Create a Planned Run in Torrent Suite™ Software
1
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
7
11. From the Kits page, select your kit.
a. Verify Flows is set to 400. Click Next.
12. Click Next until the Plan chevron displays.
a. Enter a planned run name.
b. Verify Use same reference & BED les for all barcodes is checked. (Uncheck
if your plan will use dierent references and BED les. See Appendix B for
details on sample planning.)
c. Verify Same sample for DNA and RNA is checked. (Uncheck if your plan
will use mixed samples. See Appendix B for details on sample planning.)
d. Enter the number of barcodes. You must enter at least one sample. The
Oncomine™ Focus Assay is optimized to run with six samples. See
Appendix B for tips on entering samples.
e. Verify Oncology radio buon is checked.
f.Enter Sample Names. Enter information about the sample(s) to aid
downstream analysis in Ion Reporter Software. (Sample ID and Sample
Description are the only optional elds.) Scroll to the right to see all columns
that require data entry.
g. Check DNA/RNA column. (This is autopopulated, but can be changed if
necessary.)
h. Enter Cancer Type. (This information is utilized in the Oncomine®
Knowledgebase Reporter.)
i. Enter tumor Cellularity percentage. This is required for downstream
analysis in Ion Reporter™ software.
Chapter 1 Create a Planned Run
Create a Planned Run in Torrent Suite™ Software
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Oncomine™ Focus Assay, Part III: Plan a Run User Guide
j. Check the Ion Reporter Workow column. (This is autopopulated, but
workows can be changed if necessary.)
k. Enter sample Relation. (This is autopopulated, but can be changed if
necessary.)
l. Enter Gender.
m. Enter IR Set ID. This correlates DNA and RNA sample pairs. Values must be
unique integer numbers.
n. Click Plan Run.
Chapter 1 Create a Planned Run
Create a Planned Run in Torrent Suite™ Software
1
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
9
Each planned run contains complete instructions for its samples, from
sequencing on the instrument to export of the nal results to Ion Reporter™
Software. A planned run is ready to execute on the sequencing instrument. Your
next steps are to get the Run Code from Plan > Planned Runs page. Enter that
number on the sequencing instrument to initiate the sequencing run. And nally,
to analyze the results in Ion Reporter™Software. See the Oncomine™ Focus Assay,
Part V: Variant Analysis User Guide for more information.
Create and execute a Planned Run in Torrent Suite™ Assay
Development Software
The following provides a summary of steps for creating a Planned Run in Torrent
Suite™ Assay Development Software, for Research Use Only on the Ion PGM™ Dx
System.
For more detailed instructions, see the Torrent Suite™ Assay Development Software Help,
available from within the software browser interface.
1. Sign in to the Torrent Suite™ Assay Development Software for the Torrent Server
connected to your Ion PGM™ Dx System.
2. Create the assay and library or libraries you will use in the run as described in
the Torrent Suite™ Assay Development Software Help. When seing up an assay, be
careful to select the appropriate panels and library, template, and sequencing
kits.
3. In the Libraries screen, select the library or libraries to be run by selecting
checkboxes in the list. To view only those libraries that have not yet been added
to a Planned Run, click To Be Planned above the list.
Note:
·Libraries prepared with the same assay in the same or dierent library batches
can be combined and run together, as long as the libraries have unique
Barcode IDs and the assays do not include control libraries.
·Up to 16 libraries can be sequenced in a single run.
Chapter 1 Create a Planned Run
Create and execute a Planned Run in Torrent Suite™ Assay Development Soft-
ware
1
10
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
4. Click Plan a Run.
5. In the Add New Plan dialog, enter a name for the run and select the appropriate
report template. The assay you selected when you prepared the library batch is
listed here. The library or libraries, including any control libraries required by
the assay, are also listed.
Note: To use a dierent assay, you must create a new library batch.
6. Click Save. The new Planned Run is automatically assigned a Run Short Code,
and is displayed at the top of the list in the Assay tab4Planned Runs screen.
7. Under the Actions header for the run, click Execute.
Note: If the Torrent Server has £10% free disk space, you will be alerted to clear
disk space before the run can be executed.
The Execute Planned Run dialog will open.
8. In the Tube Label eld, enter either the Library Sample Tube barcode (Ion Chef™
Instrument) or the sample tube label text (Ion OneTouch™ 2 Instrument):
• For template preparation using the Ion Chef™ Instrument, click inside the
eld and scan the barcode on the Ion Chef™ Library Sample Tube. The
barcode number will populate the eld, and will be tracked by the
instrument.
• For template preparation using an Ion OneTouch™ 2 Instrument, manually
enter the text that will be used to label the library tubes during the run. This
can be any combination of leers and numbers. This label text is tracked by
Ion PGM™ Dx System instruments, but not by non-Ion PGM™ Dx System
instruments. Note that the software will not allow use of the same Tube Label
text within 7 days.
Chapter 1 Create a Planned Run
Create and execute a Planned Run in Torrent Suite™ Assay Development Soft-
ware
1
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
11
9. If you are using the Ion OneTouch™ 2 Instrument, click inside the Template Prep
Kit barcode eld and scan or enter the barcode from the Ion OneTouch™ Select
Template Reagents box you will use in the run.
Note: If you are using the Ion Chef™ Instrument, skip this step.
IMPORTANT! Be sure to scan or enter the barcode from the actual reagents box
that will be used in the run.
10. Click Save to save your changes.
11. The Review Planned Run dialog will open. Write down the Run Short Code
and/or click the Print buon to print the scannable barcode. The code must be
entered or scanned at each instrument for tracking and verication.
12. Click Close to close the dialog and execute the run.
You can import Ion PGM™ Select Sequencing data from Torrent Suite™ Assay
Development Software into your local Ion Reporter™ server for further analysis. For
detailed instructions, see the latest Ion Reporter™ Software User Guide, available on the
Ion Community at the following link: ioncommunity.thermosher.com/docs/
DOC-9594.
Importing data
into an Ion
Reporter™ server
Chapter 1 Create a Planned Run
Create and execute a Planned Run in Torrent Suite™ Assay Development Soft-
ware
1
12
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
Make Oncomine™ Focus Assay
templates available in Torrent
Suite™ Software
The Oncomine™ templates are not enabled by default in Torrent Suite™ Software. This
appendix describes the administrator conguration step to enable these analysis
templates. These instructions are intended for users who are familiar with the Admin
Interface. Your ionadmin user account and password are required.
IMPORTANT! Changes in the admin interface can negatively impact the operation of
your server. If you are ever in doubt, cancel your changes.
Follow these steps to enable Oncomine™ analyses on your system:
1. Log into the Torrent Browser with your ionadmin account.
2. Click the admin gear menu and click Congure.
3. Scroll down to the boom of the Congure page. In the Database Administration
section, click the Admin Interface link.
A
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
13
4. Scroll down to the Rundb section and click Global congs.
5. Click the Cong link. (Your web root and site name are dierent.)
6. Scroll down to the boom of the page. Check Enable Oncomine? and click Save.
7. Click Back to Main Site to continue to work in Torrent Browser, or click Log Out
to exit.
8. Navigate to the Plan > Templates page, then select DNA and Fusions. Conrm
that the Oncomine™ templates appear in the Template Name Column.
Appendix A Make Oncomine™ Focus Assay templates available in
Torrent Suite™ Software
Create and execute a Planned Run in Torrent Suite™ Assay Development Soft-
ware
A
14
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
9. If so, you may return to your run planning.
Appendix A Make Oncomine™ Focus Assay templates available in
Torrent Suite™ Software
Create and execute a Planned Run in Torrent Suite™ Assay Development Soft-
ware
A
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
15
Sample Uploading Tips in Torrent
Suite™ Software
The following topics describe how to use sample sets and create planned runs and
templates in Torrent Suite™ Software to support Oncomine™ Focus Assay sequencing
runs. Seing up mixed samples on a chip is also described.
Create sample sets manually
1. Go to Plan4Samples and click Enter Samples Manually.
2. Click Enter New Sample. The Add Sample screen appears.
3. Dene samples as completely as possible.
B
16
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
4. Click Done. Your aributes appear on the Enter Samples table.
5. Enter additional samples.
6. If you have sample pairs, set Relationship Group numbers to reect pairs. For
example, DNA and RNA samples from the same sample would have the same
Relationship Group number.
7. Click Save Sample Set.
8. Name Sample Set or add samples to an existing sample set.
Import samples to create Sample Set
1. If you are importing a large number of samples, you can use the Sample
Sets4Import Samples from File feature.
2. Click the Sample File Format buon to download a CSV template.
3. Fill out the CSV template as completely as possible as this will save you time
during plan creation.
Recommended columns include: Sample name, Sample ID, Gender, Type
(sample type, such as self), Group (number that indicates the sample is a single
sample, pair or trio), DNA/RNA, Cancer Type, Cellularity %, Barcode Kit (use
Ion Select BC Set-1 for Oncomine™ Focus Assay), and Barcode.
Appendix B Sample Uploading Tips in Torrent Suite™ Software
Import samples to create Sample Set
B
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
17
4. Once the CSV le is completely lled out, click the Select File buon to upload
it.
5. Click Add Sample Set buon. Add Name, Group Type, and (optional)
description. Click Save & Finish.
The software automatically imports the samples into the Sample Sets table.
Create a planned run with sample set
1. Click Gear buon in Sample Set row.
2. Click Plan Run.
3. Select a Run Template to apply to this experiment. Click Plan Run.
The software advances your planned run creation to the Barcoding chevron and
automatically populates the barcodes you specied.
Appendix B Sample Uploading Tips in Torrent Suite™ Software
Create a planned run with sample set
B
18
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
Create a planned run for mixed sample set
The example below is a mixed sample set consisting of four sample pairs, two DNA
only samples and two RNA only samples.
1. Go to Plan4Samples and click Import Samples from File buon.
2. Click Sample File Format buon to download a CSV template. Fill out the CSV
template as completely as possible. Make sure to identify sample groups with
Group numbers.
3. Once the CSV le is completely lled out, click the Select File buon to upload
it. Select le. Click Open.
4. Click Add Sample Set. Enter name and group type. Click Save & Finish.
5. View samples on Sample Sets page.
Appendix B Sample Uploading Tips in Torrent Suite™ Software
Create a planned run for mixed sample set
B
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
19
6. Click Gear buon and select Plan Run.
7. Select template. Click Plan Run.
8. Review samples at the boom of the page.
9. Select appropriate Ion Reporter workows for non-pair samples.
10. Click Next. Software advances to the Projects chevron.
11. (Optional) Select a Project and click Next.
Appendix B Sample Uploading Tips in Torrent Suite™ Software
Create a planned run for mixed sample set
B
20
Oncomine™ Focus Assay, Part III: Plan a Run User Guide
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