Roche Oncology Analysis Server User guide

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Document Author: Singh, Ashla {DSSU~Pleasanton}

Business Area / Unit: Global Platforms & Support

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Document Type: Device Master Record

Document Creator: Wylie, Denise {DSSD~Pleasanton}

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Document Title: 04765.01_UG_Software-User-Guide

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Global Group: Product Documentation

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Language: English

Site: Pleasanton

Document Description: AVENIO Oncology Analysis SW User Guide v1.2 SW v2.0.0

Description of change: Updated note regarding germline variants with high allele

frequency in “Interpreting the variant report” on page 56. Added

statement that the AVENIO Oncology Analysis Software is for

research use only.

Project: N.SU.04765.01

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Signed By: singha78 (Ashla Singh {DSSUA})

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Signed Date: 09-Feb-2021 18:08:53 (UTC)

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

AVENIO Oncology Analysis Software

User Guide

Version 1.2

Software Version 2.0.0

For Research Use Only. Not for use in diagnostic procedures.

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2 AVENIO Oncology Analysis Software User Guide, v1.2

Publication information

Document material number: 08743045001.

Edition notice

This publication is intended for users of AVENIO Oncology Analysis Software.

Every effort has been made to ensure that all the information contained in this publication is correct at the time of publishing. However, the

manufacturer of this product may need to update the publication information as output of product surveillance activities, leading to a new version of

this publication.

Where to find information

This guide contains information about using the analysis software, organized according to the normal operation workflow.

The AVENIO Oncology Analysis Software Admin Guide contains information about setting up and managing the analysis software for users.

The AVENIO Tumor Tissue Analysis Kits Reagent Workflow User Guide contains information about using the reagents, organized according to the

normal operation workflow.

The AVENIO ctDNA Analysis Kits Reagent Workflow User Guide contains information about using the reagents, organized according to the normal

operation workflow.

General attention

To avoid incorrect results, ensure that you are familiar with the instructions and safety information.

 Pay particular attention to all safety notices.

 Always follow the instructions in this publication.

 Do not use the software in a way that is not described in this publication.

 Store all publications in a safe and easily retrievable place.

Training

Do not carry out operation tasks or maintenance actions unless you have received training from Roche. Leave tasks that are not described in the user

documentation to trained Roche Service representatives.

Screenshots

The screenshots in this publication have been added exclusively for illustration purposes. Configurable and variable data, such as tests, results, or path

names visible therein must not be used for laboratory purposes.

Warranty

Any customer modification to the system renders the warranty or service agreement null and void.

For conditions of warranty, contact your local sales representative, or refer to your warranty contract partner.

Always leave software updates to a Roche Service representative, or perform such updates with their assistance.

Publication version Software version Revision date Change description

1.0 2.0.0 September 2018 First version.

1.1 2.0.0 June 2019 Clarified information and instructions, and removed

Variant calling errors from Appendix A, Troubleshooting.

1.2 2.0.0 February 2021 Updated note regarding germline variants with high allele

frequency, and made minor corrections.

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Publication information

AVENIO Oncology Analysis Software User Guide, v1.2 3

Copyright

License information

AVENIO Oncology Analysis Software is protected by contract law, copyright and other intellectual property laws, and international treaties.

AVENIO Oncology Analysis Software is subject to an end user license agreement and only authorized users may access and use the software.

Unauthorized distribution or other uses may result in civil or criminal liability.

Open source and commercial software

The AVENIO Oncology Analysis Software may include third-party commercial or open source software. For further information on such software,

including applicable license terms and conditions, refer to the associated product documentation.

This open source and commercial software and AVENIO Oncology Analysis Software as a whole can constitute a device regulated in accordance with

applicable law. For more detailed information, refer to the user manual and labeling.

Please note that the respective authorization is no longer valid according to the corresponding legislation should any unauthorized changes be made to

AVENIO Oncology Analysis Software.

Trademarks

The following trademarks are acknowledged:

AVENIO is a trademark of Roche.

All other trademarks are the property of their respective owners.

Patent license limitations

For patent license limitations, go to www.technical-support.roche.com and search by product name or product material number. License disclaimers are

listed at the bottom of the Basics tab.

Feedback

Every effort has been made to ensure that this publication fulfills the intended use. All feedback on any aspect of this publication is welcome and is

considered during updates. Contact your Roche representative, should you have any such feedback.

Contact addresses

Technical support

For product-related technical documents or to contact Roche Technical Support, go to sequencing.roche.com/support.

Manufacturer

Roche Molecular Systems, Inc.

1080 US Highway 202 South

Branchburg, NJ 08876

USA

Distribution Roche Diagnostics GmbH

Sandhofer Strasse 116

68305 Mannheim

Germany

Distribution in USA Roche Diagnostics

9115 Hague Road

Indianapolis, Indiana 46256

USA

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AVENIO Oncology Analysis Software User Guide, v1.2 5

Table of contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Regulatory disclaimer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

AVENIO Tumor Tissue Analysis Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

AVENIO ctDNA Analysis Kits. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

AVENIO Oncology Analysis Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Symbols, abbreviations, and acronyms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

AVENIO Oncology Analysis Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Symbols used in this publication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Abbreviations and acronyms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

What is new in publication version 1.2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Chapter 1. Getting started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

About AVENIO Oncology Analysis Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Logging on to the analysis software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

To log on . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Changing your password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

To change your password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Resetting your password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

To reset your password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Changing your display name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

To change your display name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Updating your email address. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

To update your email address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Viewing the analysis software and database versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

To view the analysis software and database versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Accessing support documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

To access support documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Logging off of the analysis software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

To log off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Chapter 2. Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17

Analysis software user interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Overview of the analysis software process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Enter sample information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Choose sequencing output files and start analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

View sample results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Create Concordance analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

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6 AVENIO Oncology Analysis Software User Guide, v1.2

Chapter 3. Create secondary analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

Creating a secondary analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Creating a secondary analysis manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

To create a secondary analysis manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Creating an analysis using the CSV template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Choosing the analysis input file and starting analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Editing sample information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Setting the output directory for Analysis files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Viewing a list of secondary analyses and status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

To view a list of secondary analyses and status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Analyses status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Viewing secondary analysis results and sample data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

To view secondary analysis results and sample data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Searching for an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

To search for an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Deleting an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

To delete an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Cancelling a queued or in-progress analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

To cancel a queued or in-progress analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Duplicating and rerunning an analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

To duplicate and rerun an analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Chapter 4. Create concordance analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41

Creating a concordance analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

To create a concordance analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Chapter 5. View sample results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45

Viewing SNV and Indel results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

To view SNV and Indel results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Viewing individual variant information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

To view individual variant information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Viewing CNVs and fusions results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

To view CNV and fusion results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Viewing Loci of interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

To view the Loci of interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Chapter 6. Generate reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53

Viewing an auto-generated report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

To view an auto-generated report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Viewing sample metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

To view sample metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Sample Metrics report interpretation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

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AVENIO Oncology Analysis Software User Guide, v1.2 7

Interpreting the variant report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Sample details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Variant details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Generating custom reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

To apply a saved filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

To create a custom filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Chapter 7. View output files and analysis metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63

Viewing analysis metadata. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

To view analysis metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Viewing sample metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

To view sample metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Viewing output files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

To view output files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Appendix A. Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67

User input errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

System errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

To troubleshoot system errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Workflow errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

To troubleshoot workflow errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Duplicate and Rerun error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Error information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Downloading error logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Appendix B. Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73

Appendix C. Converting BCL output to FASTQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75

To convert a BCL file to FASTQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

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AVENIO Oncology Analysis Software User Guide, v1.2 9

Preface

Regulatory disclaimer

For Research Use Only. Not for use in diagnostic procedures.

AVENIO Tumor Tissue Analysis Kits

The AVENIO Tumor Tissue Analysis Kits include the reagents needed to isolate DNA from FFPE tissue, prepare sequencing libraries, and enrich

selected regions of interest using one of three panel options:

 AVENIO Tumor Targeted Panel (17 genes)

 AVENIO Tumor Expanded Panel (77 genes)

 AVENIO Tumor Surveillance Panel (197 genes)

These ready-to-use kits use a hybrid-capture based workflow to profile the genomics of DNA derived from solid tumor FFPE tissue. The AVENIO Tumor

Tissue Analysis Kits help labs consistently purify and enrich targeted regions in solid tumor FFPE DNA for sequencing. The AVENIO Tumor Tissue

Analysis Kits provide lab professionals the ability to generate insights from all four mutation classes—SNVs, Indels, CNVs, and fusions—using a DNA-

only workflow. Each kit includes reagents for processing up to 24 reactions in a single sequencing run on a NextSeq 500/550.

AVENIO ctDNA Analysis Kits

The AVENIO ctDNA Analysis Kits are a portfolio of three next-generation sequencing liquid biopsy assays designed to help researchers understand the

genomic complexity of aberrations in solid tumors. The kits are for research use only, not for use in diagnostic procedures. The AVENIO ctDNA Analysis

Kits provide an end-to-end tumor profiling and monitoring solution, from cfDNA extraction to analysis and variant reporting.

AVENIO Oncology Analysis Software

AVENIO Oncology Analysis Software enables the end-to-end workflow. The software is for research use only. The AVENIO Oncology Analysis Software

allows labs to quickly and easily transform data from enriched DNA and ctDNA processed on an Illumina NextSeq into meaningful insights for profiling

mutations and monitoring how they evolve over time.

The AVENIO Oncology Analysis Software is run on a server that is connected to on-premise shared network storage. The Oncology Analysis Server is

required and available from Roche. After the AVENIO Oncology Analysis Software completes the workflow and report, the shared network storage will

contain both the sequencing output files and the analysis output files.

Symbols, abbreviations, and acronyms

AVENIO Oncology Analysis Software

Except where the context clearly indicated otherwise, the following product names and descriptors are used.

An on-premise Oncology Analysis Server (OAS) allows lab professionals to produce secondary analysis variant calls locally,

review QC metrics, and run analytical concordance reports. The OAS runs the AVENIO Oncology Analysis Software and is

necessary to provide analysis setup and reporting functionality for the entire AVENIO family of next-generation oncology

assays. The OAS is available for purchase from Roche.

Product name Descriptor

AVENIO Oncology Analysis Software analysis software

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What is new in publication version 1.2

10 AVENIO Oncology Analysis Software User Guide, v1.2

Symbols used in this publication

Abbreviations and acronyms

The following abbreviations and acronyms are used.

What is new in publication version 1.2

 Updated note regarding germline variants with high allele frequency in “Interpreting the variant report” on page 56.

 Added statement that the AVENIO Oncology Analysis Software is for research use only.

Symbol Explanation

Important note: Highlights information that is critical for optimal performance of the system. May also indicate that loss of data or

invalid data could occur if the precautions or instructions are not observed.

Information note: Identifies items of general interest and additional information about the topic or procedure being described.

Abbreviation/acronym Definition

AF Allele Frequency or Allele Fraction

BCL Base Call File

Bfx Bioinformatics

cfDNA cell free DNA

CNV Copy Number Variant

ctDNA circulating tumor DNA

DNA DeoxyriboNucleic Acid

GE Genome Equivalent

GID Group ID

Indel Insertion or deletion

LOD Limit of Detection

NFS Network File System

PPA Percent Positive Agreement

SNV Single Nucleotide Variant

UID User ID

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Chapter 1. Getting started

AVENIO Oncology Analysis Software User Guide, v1.2 11

Chapter 1. Getting started

This guide includes information and instructions for using the AVENIO Oncology Analysis Software to create and manage

analyses, view sample results, manage reports, and view output files and analysis metadata. This guide also includes general

troubleshooting information and methodology.

About AVENIO Oncology Analysis Software

AVENIO Oncology Analysis Software enables the end-to-end workflow. The software is for research use only. The AVENIO

Oncology Analysis Software allows labs to quickly and easily transform data from enriched DNA and ctDNA processed on an

Illumina NextSeq into meaningful insights for profiling mutations and monitoring how they evolve over time.

The AVENIO Oncology Analysis Software is run on a server that is connected to on-premise shared network storage. The

Oncology Analysis Server is required and available from Roche. After the AVENIO Oncology Analysis Software completes the

workflow and report, the shared network storage will contain both the sequencing output files and the analysis output files.

Logging on to the analysis software

Prerequisites

 Your admin set up user accounts for your system.

 Google Chrome version 59.0.3071.115 or later is installed.

 Your admin provided you with the analysis software URL.

To log on

1. Open your Chrome browser, and navigate to the analysis software URL provided to you by your admin.

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Logging on to the analysis software

12 AVENIO Oncology Analysis Software User Guide, v1.2

The first time you open the URL, you will get a privacy message similar to the one below but with a different IP address.

2. Choose Advanced.

3. Choose the link Proceed to <your IP address> (unsafe).

The analysis software opens to the log on page.

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Chapter 1. Getting started

AVENIO Oncology Analysis Software User Guide, v1.2 13

4. Enter your credentials. (If you forgot your password, see “Resetting your password ” on page 14.)

5. Accept the Terms and Conditions.

6. Choose Log on.

The analysis software opens to the Secondary analyses tab.

Changing your password

To change your password

1. Log on to the analysis software.

2. At the upper right corner of any page, choose the user drop-down menu, and choose My account.

If you reset your browser cache or use a new browser, you will need to accept the Terms and

Conditions again before logging on to the system.

Users are automatically logged out after 24 hours.

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Resetting your password

14 AVENIO Oncology Analysis Software User Guide, v1.2

3. Change your password, as desired.

4. Choose Save password.

Resetting your password

If you forgot your password, you can reset it on the analysis software logon page.

To reset your password

1. On the analysis software logon page, choose Forgot password?

2. Enter your user name or email address, and choose Send link.

You will receive an email with a link to reset your password. Follow the instructions in the email.

This feature is only available if the SMTP server is configured correctly.

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Chapter 1. Getting started

AVENIO Oncology Analysis Software User Guide, v1.2 15

Changing your display name

You can change the way your name appears to others in the analysis software.

To change your display name

1. At the upper right corner of any page, choose the user drop-down menu, and choose My account.

2. Change your Real name, as desired.

3. Choose Save changes.

Updating your email address

The analysis software uses email for logging on to the software, resetting passwords, and sending automatic

analysis-complete notifications. You can update your email address at any time.

To update your email address

1. At the upper right corner of any page, choose the user drop-down menu, and choose My account.

2. Update your email address, as needed.

3. Choose Save changes.

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Viewing the analysis software and database versions

16 AVENIO Oncology Analysis Software User Guide, v1.2

Viewing the analysis software and database versions

You may be asked by Technical Support to provide the version numbers of the analysis software and the databases

you are using.

To view the analysis software and database versions

1. Log on to the analysis software.

2. At the upper right corner of any page, choose the user drop-down menu, and choose About.

Accessing support documentation

You can access the product user guide and other support documentation from the analysis software.

To access support documentation

At the upper right corner of any page, choose the Help Center drop-down menu, choose either User guide or Support docs,

and navigate to the desired document.

Logging off of the analysis software

To log off

At the upper right corner of any page, choose the user drop-down menu, and choose Log off.

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Chapter 2. Overview

AVENIO Oncology Analysis Software User Guide, v1.2 17

Chapter 2. Overview

Analysis software user interface

The analysis software includes the following main structure:

 Global navigation toolbar: The toolbar is located at the top of every page of the analysis software.

 Home button – The home button is located at the top left of every page in the analysis software. Choose the

Home button to go to the Secondary analyses tab.

 Help Center drop-down menu – This menu includes a link to the user guide and other support documents that are

relevant to the analysis software.

 User drop-down menu – This menu includes account information for the logged-on user, software and database

version information, and an option for logging off of the analysis software.

 Main tabs: The main tabs are located below the toolbar on every page of the analysis software. There are 3 main tabs:

 Secondary analyses tab – This tab opens when you log on to the analysis software and includes:

 Search analyses field – Use this field to search for a secondary analysis. Choose the Advanced drop-down menu

to narrow your search results.

 Create new analysis button – Choose this button to create a new secondary analysis.

 Secondary analyses table – View a list of all secondary analyses along with the status, number of samples in an

analysis, sample type, user who last made changes to the analysis (if the analysis is not in Draft or Cancelled state)

date and time the analysis was edited, and the owner of the analysis.

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Analysis software user interface

18 AVENIO Oncology Analysis Software User Guide, v1.2

 Completed samples tab – This tab includes:

 Search samples field – Use this field to search for a sample. Choose the Advanced drop-down menu to narrow

your search results.

 Completed samples table – View a list of completed samples included in all secondary analyses along with sample

ID, analysis name, date and time the analysis was completed, subject ID, owner of the analysis, and sample type.

 Concordance analyses tab – This tab includes:

 Search concordance analyses field – Use this field to search for a concordance analysis. Choose the Advanced

drop-down menu to narrow your search results.

 Create concordance analysis field – Choose this button to create a new concordance analysis.

 Concordance analyses table – View a list of the concordance analyses along with the analysis name, status, filter

set used, number of pairs, date and time the analysis was submitted, and owner of the analysis.

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Roche Oncology Analysis Server User guide

Roche Oncology Analysis Server User guide

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