Thermo Fisher Scientific Oncomine Focus Assay, Part III: Plan a Run User guide

Brand: Thermo Fisher Scientific

Model: Oncomine Focus Assay, Part III: Plan a Run

Type: User guide

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

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.

Corporate entity

Life Technologies | Carlsbad, CA 92008 USA | Toll Free in USA 1 800 955 6288

TRADEMARKS

All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed.

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

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,

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.

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 workow, 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 buon to access the Copy function.

6. (Optional) Dene 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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

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 congured, congure it through Ion

Reporter Congure seings. See Congure 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

workow from the Existing Workow drop-down menu.

Chapter 1 Create a Planned Run

Create a Planned Run in Torrent Suite™ Software

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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

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 dierent 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 buon 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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

j. Check the Ion Reporter Workow column. (This is autopopulated, but

workows 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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

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 seing 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 dierent 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

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 dierent 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 leers 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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

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 buon to print the scannable barcode. The code must be

entered or scanned at each instrument for tracking and verication.

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.thermosher.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

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 conguration 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 Congure.

3. Scroll down to the boom of the Congure page. In the Database Administration

section, click the Admin Interface link.

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

4. Scroll down to the Rundb section and click Global congs.

5. Click the Cong link. (Your web root and site name are dierent.)

6. Scroll down to the boom 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. Conrm

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

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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

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. Seing 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. Dene samples as completely as possible.

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

4. Click Done. Your aributes appear on the Enter Samples table.

5. Enter additional samples.

6. If you have sample pairs, set Relationship Group numbers to reect 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 buon 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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

4. Once the CSV le is completely lled out, click the Select File buon to upload

it.

5. Click Add Sample Set buon. 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 buon 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 specied.

Appendix B Sample Uploading Tips in Torrent Suite™ Software

Create a planned run with sample set

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 buon.

2. Click Sample File Format buon 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 buon 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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

6. Click Gear buon and select Plan Run.

7. Select template. Click Plan Run.

8. Review samples at the boom of the page.

9. Select appropriate Ion Reporter workows 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

Oncomine™ Focus Assay, Part III: Plan a Run User Guide

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