Roche AVENIO Oncology Analysis SW Admin User manual

Brand: Roche

Model: AVENIO Oncology Analysis SW Admin

Type: User manual



AVENIO Oncology Analysis Software

Admin Guide

Version 1.1

Software Version 2.0.0

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

2AVENIO Oncology Analysis Software Admin Guide, v1.1

Publication information

Document material number: 08743053001

Edition notice

This publication is intended for administrators 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 setting up and managing the analysis software for users.

The AVENIO Oncology Analysis Software User Guide contains information about using the analysis software, organized according to the normal

operation workflow.

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 April 2019 Clarified a prerequisite for logging on to the analysis software.

Publication information

AVENIO Oncology Analysis Software Admin Guide, v1.1 3

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 and COBAS are trademarks 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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4AVENIO Oncology Analysis Software Admin Guide, v1.1

AVENIO Oncology Analysis Software Admin Guide, v1.1 5

Table of contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

Regulatory disclaimer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

AVENIO Tumor Tissue Analysis Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

AVENIO ctDNA Analysis Kits. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

AVENIO Oncology Analysis Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Symbols, abbreviations, and acronyms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

AVENIO Oncology Analysis Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Symbols used in the publication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Abbreviations/acronyms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

What is new in publication version 1.1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Loss of data integrity or unavailability of the system due to malicious software or unauthorized

system access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

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

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

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

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

Navigating the user interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Logging off of the analysis software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

To log off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Chapter 2. Manage custom annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

About custom annotations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Creating custom annotations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

To create a custom annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Custom VCF annotation file headers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Editing a custom annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

To edit a custom annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Archiving a custom annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

To archive a custom annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Restoring an archived custom annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

To restore an archived custom annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Chapter 3. Manage filter sets for reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Creating a filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

To create a filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Editing a filter set. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

To edit a filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

6AVENIO Oncology Analysis Software Admin Guide, v1.1

Archiving a filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

To archive a filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Restoring an archived filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

To restore an archived filter set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Chapter 4. Manage users. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Adding a new user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

To add a new user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Editing a user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

To edit a user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Setting or resetting user passwords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

To generate a link . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Archiving an user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Restoring an archived user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

To restore an archived user . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Chapter 5. Configure the analysis software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29

Setting up shared storage locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

To set up shared storage locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Setting wait timeout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

To set wait timeout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Choosing the path to the bcl2fastq folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

To choose the path to the bcl2fastq folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Downloading error logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

To download error logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Workflow errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

System errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

AVENIO Oncology Analysis Software Admin Guide, v1.1 7

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 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

What is new in publication version 1.1

8AVENIO Oncology Analysis Software Admin Guide, v1.1

Symbols used in the publication

Abbreviations/acronyms

The following abbreviations and acronyms are used.

What is new in publication version 1.1

Clarified a prerequisite for logging on to the analysis software (see “Logging on to the analysis software” on page 11)

Loss of data integrity or unavailability of the system due to malicious software

or unauthorized system access

To avoid infection of malicious software or the unauthorized misuse of the system, the following recommendations are essential:

Make sure other computers and services on the network (for example: the LIS, archiving share or -service, backup share or -service) are

properly secured and protected against malicious software and unauthorized access.

Laboratory IT is responsible for the security of their local area network, especially in protecting it against malicious software and attacks.

This protection might include measures, such as a firewall, to separate the device from uncontrolled networks as well as measures that

ensure that the connected network is free of malicious code.

Check all external storage devices, like CDs, DVDs, or USB mass storage devices with an anti-virus scanner (on another computer) to ensure that

they are free of malicious software before using them on the system.

Restrict physical access to the system and all attached IT infrastructure (computer, cables, network equipment, etc.).

Make sure that system backups and archive files are protected from any unauthorized access and disaster, this includes: remote storage location;

disaster recovery sites; and secure transfer of backup files.

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

BCL Base Call File

cfDNA cell free DNA

ctDNA circulating tumor DNA

DNA DeoxyriboNucleic Acid

GID Group ID

Indel Insertion or deletion

NFS Network File System

RSR Roche Service representative

SNV Single Nucleotide Variant

UID User ID

Chapter 1. Getting started

AVENIO Oncology Analysis Software Admin Guide, v1.1 11

Chapter 1. Getting started

This guide provides instructions for setting up and managing the AVENIO Oncology Analysis Software for your users.

About AVENIO Oncology Analysis Software

AVENIO Oncology Analysis Software enables the end-to-end workflow. 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

The Roche Service representative (RSR) has set up an administrator account for your system.

Google Chrome browser version 59.0.3071.115 or later is installed.

You have 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.

Logging on to the analysis software

12 AVENIO Oncology Analysis Software Admin Guide, v1.1

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.

Chapter 1. Getting started

AVENIO Oncology Analysis Software Admin Guide, v1.1 13

4. Enter your credentials.

5. Accept the Terms and Conditions.

6. Choose Log On.

The analysis software opens to the Secondary analyses tab.

7. For admin functions, on the toolbar, choose Administrator > Settings.

The analysis software opens to the About page.

For information on changing your password, display name, and email address, refer to the AVENIO Oncology Analysis

Software User Guide.

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.

Navigating the user interface

14 AVENIO Oncology Analysis Software Admin Guide, v1.1

Navigating the user interface

Admin functions are available on the Settings page. To access the Settings page, on the toolbar, choose the user drop-down

menu, and choose Settings.

Logging off of the analysis software

To log off

On the toolbar, choose the user drop-down menu, and choose Log off.

Tasks Menu item

Application

View version information for the analysis software and variant databases. About

Search for users, view a list of active and archived users, create a user, archive a user, and

restore an archived user to active.

Users

View a list of active shared storage locations and archived locations, map a new location,

archive a location, and restore an archived location to active.

Shared storage

Workflows

View a list of active and inactive panels, archive a panel, and restore an archived panel. Panels

View a list of active and inactive custom annotations, create a custom annotation, archive a

custom annotation, and restore an archived annotation.

Custom annotations

View a list of active and inactive filter sets, archive a filter set, and restore an archived filter set. Filter sets

Choose the maximum time that a sequencing analysis will wait for the sequencer to complete

and transfer the BCL, and choose the folder where you placed the extracted bcl2fastq binary.

Configuration

Chapter 2. Manage custom annotations

AVENIO Oncology Analysis Software Admin Guide, v1.1 15

Chapter 2. Manage custom annotations

About custom annotations

If you choose to have your own annotation database, you can upload the VCF file that represents the list of variants with

annotations then attach the annotation file to a workflow. When a user chooses that workflow to be used as part of analysis,

any variant that appears in that custom VCF will be annotated with the custom database.

Custom annotations apply for only SNV and Indels and are included in the report. Indel custom annotations refer to those

indels within the loci of interest. Variants associated with a custom annotation are reflected as a black dot in the user portion of

the software, where a user is viewing the reported variants for analysis. The user can choose the custom annotation for a

particular analysis workflow.

The following example for BRAF has a custom annotation as depicted with a black dot.

About custom annotations

16 AVENIO Oncology Analysis Software Admin Guide, v1.1

Custom annotation details appear in the BRAF variant information card.

Chapter 2. Manage custom annotations

AVENIO Oncology Analysis Software Admin Guide, v1.1 17

Creating custom annotations

You can create a custom annotation to define a set of variants of interest. This list of variants will be used to annotate reported

variants if linked to an analysis workflow. Any sample that is analyzed using that workflow will be annotated for the variants

when present in the sample-included in the custom annotation file. Indel custom annotations refer to those indels within the

loci of interest.

To create a custom annotation

1. On the toolbar, choose the user drop-down menu, and choose Settings > Custom annotations.

2. Choose Create custom annotation.

3. Enter the name and description.

4. Choose your custom annotation VCF file.

5. If desired, choose the Set as default check box.

6. Choose Save.

The custom annotation is added to the Custom annotations table.

Upload the custom annotation to the network mount. Do not upload the file locally.

Creating custom annotations

18 AVENIO Oncology Analysis Software Admin Guide, v1.1

Custom VCF annotation file headers

When creating a custom VCF annotation file, verify that the VCF does not contain field names or headers that conflict with

the Roche annotation pipeline:

##INFO=<ID=IN_COSMIC,Number=0,Type=Flag,Description="Variant exists in COSMIC">

##INFO=<ID=COSMIC_ID,Number=.,Type=String,Description="Corresponding ids in COSMIC">

##INFO=<ID=COSMIC_SITE,Number=.,Type=String,Description="Primary sites associated with this

variant in COSMIC"> ##INFO=<ID=COSMIC_SITE_COUNT,Number=.,Type=Integer,Description="Comma

separated number of times that this variant appears in COSMIC per primary site. Index of primary

sites is as follows:

adrenal_gland=0,autonomic_ganglia=1,biliary_tract=2,bone=3,breast=4,central_nervous_system=5,

cervix=6,endometrium=7,eye=8,fallopian_tube=9,gastrointestinal_tract=10,genital_tract=11,haem

atopoietic_and_lymphoid_tissue=12,kidney=13,large_intestine=14,liver=15,lung=16,meninges=17,N

S=18,oesophagus=19,ovary=20,pancreas=21,paratesticular_tissues=22,parathyroid=23,penis=24,per

itoneum=25,pituitary=26,placenta=27,pleura=28,prostate=29,retroperitoneum=30,salivary_gland=3

Upload the custom annotation to the network mount. Do not upload the file locally.

Manage custom annotations15

1,skin=32,small_intestine=33,soft_tissue=34,stomach=35,testis=36,thymus=37,thyroid=38,upper_a

erodigestive_tract=39,urinary_tract=40,vagina=41,vulva=42"> ##INFO=<ID=COSMIC_COUNT,Number=

1,Type=Integer,Description="Number of times variant appears in COSMIC"> ##INFO=<ID=COSMIC_

SITE_COUNT_SOMATIC,Number=.,Type=Integer,Description="Comma separated number of times

that this somatic variant appears in COSMIC per primary site. Index of primary sites is as follows:

adrenal_gland=0,autonomic_ganglia=1,biliary_tract=2,bone=3,breast=4,central_nervous_system=5,

cervix=6,endometrium=7,eye=8,fallopian_tube=9,gastrointestinal_tract=10,genital_tract=11,haem

atopoietic_and_lymphoid_tissue=12,kidney=13,large_intestine=14,liver=15,lung=16,meninges=17,N

S=18,oesophagus=19,ovary=20,pancreas=21,paratesticular_tissues=22,parathyroid=23,penis=24,per

itoneum=25,pituitary=26,placenta=27,pleura=28,prostate=29,retroperitoneum=30,salivary_gland=3

1,skin=32,small_intestine=33,soft_tissue=34,stomach=35,testis=36,thymus=37,thyroid=38,upper_a

erodigestive_tract=39,urinary_tract=40,vagina=41,vulva=42"> ##INFO=<ID=IN_DBSNP,Number=

0,Type=Flag,Description="Variant exists in DBSNP"> ##INFO=<ID=DBSNP_ID,Number=.,

Type=String,Description="DBSNP id">

##INFO=<ID=DBSNP_COMMON,Number=.,Type=Integer,Description="Common variant in DBSNP">

##INFO=<ID=DBSNP_AF,Number=.,Type=Float,Description="Allele frequency in DBSNP">

##INFO=<ID=DBSNP_AQ,Number=.,Type=Integer,Description="Alignment quality in DBSNP. 1=unique

mapping, 2=non-unique, 3=many matches"> ##INFO=<ID=IN_TCGA,Number=0,Type=Flag,Description="

Variant exists in TCGA"> ##INFO=<ID=TCGA_TYPES,Number=.,Type=String,Description="Cancer

types associated with this variant in TCGA">

##INFO=<ID=TCGA_COUNT,Number=1,Type=Integer,Description="Number of times variant appears in

TCGA"> ##INFO=<ID=TCGA_TYPE_COUNTS,Number=.,Type=Integer,Description="Comma separated number

of times that this variant appears in TCGA per cancer type. Index of cancer types is as follows:

LAML=0,ACC=1,BLCA=2,LGG=3,BRCA=4,CESC=5,CHOL=6,COAD=7,ESCA=8,FPPP=9,GBM=10,HNSC=11,KICH=12,KI

RC=13,KIRP=14,LIHC=15,LUAD=16,LUSC=17,DLBC=18,MESO=19,OV=20,PAAD=21,PCPG=22,PRAD=23,READ=24,S

ARC=25,SKCM=26,STAD=27,TGCT=28,THYM=29,THCA=30,UCS=31,UCEC=32,UVM=33"> ##INFO=<ID=IN_KG,Number=

0,Type=Flag,Description="Variant exists in 1000 Genomes"> ##INFO=<ID=KG_AF,Number=

A,Type=Float,Description="Allele frequency in 1000 Genomes">

##INFO=<ID=KG_AFR_AF,Number=A,Type=Float,Description="Allele frequency in the AFR population

in 1000 Genomes"> ##INFO=<ID=KG_EAS_AF,Number=A,Type=Float,Description="Allele frequency in

the EAS population in 1000 Genomes"> ##INFO=<ID=KG_AMR_AF,Number=A,Type=Float,Description="

Allele frequency in the AMR population in 1000 Genomes"> ##INFO=<ID=KG_SAS_AF,Number=

A,Type=Float,Description="Allele frequency in the SAS population in 1000 Genomes">

##INFO=<ID=KG_EUR_AF,Number=A,Type=Float,Description="Allele frequency in the EUR population

in 1000 Genomes"> ##INFO=<ID=IN_EXAC,Number=0,Type=Flag,Description="Variant exists in EXAC">

##INFO=<ID=EXAC_AF_FIN,Number=A,Type=Float,Description="Allele frequency in the FIN population

in EXAC"> ##INFO=<ID=EXAC_AF_OTH,Number=A,Type=Float,Description="Allele frequency in the

OTH population in EXAC"> ##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele frequency

in EXAC"> ##INFO=<ID=EXAC_AF_AFR,Number=A,Type=Float,Description="Allele frequency in the AFR

population in EXAC"> ##INFO=<ID=EXAC_AF_EAS,Number=A,Type=Float,Description="Allele frequency

in the EAS population in EXAC"> ##INFO=<ID=EXAC_AF_NFE,Number=A,Type=Float,Description="

Allele frequency in the NFE population in EXAC">

##INFO=<ID=EXAC_AF_AMR,Number=A,Type=Float,Description="Allele frequency in the AMR population

in EXAC"> ##INFO=<ID=EXAC_AF_SAS,Number=A,Type=Float,Description="Allele frequency in the

SAS population in EXAC">

Chapter 2. Manage custom annotations

AVENIO Oncology Analysis Software Admin Guide, v1.1 19

Editing a custom annotation

To edit a custom annotation

1. On the toolbar, choose the user drop-down menu, and choose Settings > Custom annotations.

2. Choose the annotation of interest.

3. Edit the information, as needed.

4. Choose Save.

Archiving a custom annotation

To archive a custom annotation

1. On the toolbar, choose the user drop-down menu, choose Settings > Custom annotations.

2. For the annotation of interest, choose Archive custom annotation .

The following confirmation message appears.

3. Choose Archive annotation.

The annotation is moved to the Archived custom annotation table.

Restoring an archived custom annotation

20 AVENIO Oncology Analysis Software Admin Guide, v1.1

Restoring an archived custom annotation

To restore an archived custom annotation

1. On the toolbar, choose the user drop-down menu, and choose Settings > Custom annotations.

2. Choose Restore custom annotation to active .

The annotation is moved to the Custom annotations table.

Chapter 3. Manage filter sets for reports

AVENIO Oncology Analysis Software Admin Guide, v1.1 21

Chapter 3. Manage filter sets for reports

The analysis software includes one RocheDefault filter set for reports; however, you can create additional filter sets for your

users. You can edit the description and default status of any filter set in the analysis software. You can also archive any filter set

and restore an archived filter set, if needed.

Creating a filter set

To create a filter set

1. Choose the Completed samples tab.

2. Choose the sample of interest.

Creating a filter set

22 AVENIO Oncology Analysis Software Admin Guide, v1.1

3. Choose Select filter set or report > Custom filter set.

4. Choose the filters you want to apply.

Known somatic

Choose somatic variants to keep found in:

COSMIC. Confirmed somatic in COSMIC, with number of samples greater than x

TCGA with number of samples greater than y

AND

Rare in germline

Choose how to remove variants found in one of the following:

1000 Genomes above a certain allele frequency

ExAC above a certain allele frequency

dbSNP common SNPs

AND

Matches custom annotation: This option includes variants that are found only within the custom annotation file.

If no custom annotation file was used as part of the analysis workflow, setting this option will have no effect; however,

you can still use the custom annotation filter and save it for a future filter set. To see if a custom annotation file was

used, review the sample metadata.

Filtering for Rare in germline, Known somatic, and Matches custom annotation use logical and

operation filtering criteria.

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Roche AVENIO Oncology Analysis SW Admin User manual

Roche AVENIO Oncology Analysis SW Admin User manual

Roche AVENIO Oncology Analysis SW Admin User manual

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