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Download both of the license files (.bin) from the Illumina welcome email to your laptop.
Launch the application in browser based on the Info message provided during the time of successful installation in the nohup.out file, either with the Fully Qualified domain name (Example: hostname.domainname.com) or with the Static IP address. Once application is launched, you will see a message in the browser "Your connection is not private". This message is shown because the application is configured with a self signed certificate which auto renews periodically. To bypass this message from the browser, refer to How to section under the section "Add Certificate to the Trusted sites". Or alternatively if you do not want to "Add this certificate to the Trusted sites", you can click on Advanced button in the browser and then select proceed to the url. Application will then get launched where it would ask you to upload the License File.
Upload the license file which has the name 'ConnectedInsightsSetupLicense.bin' in it from the browse button. This provides access to Connected Insights - Local software. The installation of license shall be very quick. After installation is complete, you will see a pop-up message which says "License Installation is successful" and you will be redirected to the login screen. You can dismiss the message. Proceed to next step which is Step 4 of Software Installation (New customers)
Note: If the license file installation fails, a failure message displays, and you will not be able to use the application. If a failure occurs you will see any one of these messages, refer to Installation Status Messages. To recover, contact Illumina support team.
Connected Insights - Local software provides status messages during the installation process. These messages indicate that the installation has passed, failed, or has errors that prevent it from continuing. The detailed installer log is at /var/log/ici_installer.log
.
The following messages are related to the installation of the Connected Insights - Local software:
If the installation is successful, the following message displays:
– Success: Illumina Connected Insights software installation is successful.
If the installation fails, the following message displays with information on how to troubleshoot the installation issues:
– Failed: Illumina Connected Insights software installation has failed, unable to start one or more services. Please visit troubleshooting section of the product documentation or contact service and support team.
If errors occur before or during installation, the following messages display with information on how to resolve the errors:
– Error: DRAGEN server v4 check failed. Please run this script on DRAGEN v4 server only. Installation is aborted.
– Error: Unsupported Operating system. Oracle Linux 8 Operating System is required to install this Software. Installation is aborted.
– Error: Memory space check failed. /staging on DRAGEN server v4 needs 200GB or more free space to install the Software. Installation is aborted
.
The following messages are related to the installation of the Connected Insights - Local software license file:
If the installation is successful, the following message displays:
The license was installed successfully
If the License installation fails, application displays appropriate error message with the reason for the failure:
– If the License is corrupted or a unsupported .bin file is selected:
The License file is Invalid
– If the License has expired:
The License file is expired
– If License file is not intended for the current DRAGEN server v4:
The license file in not intended for this DRAGEN server v4.
– If the selected license file is a Quota License file instead of Setup:
The License provided is a renewal License file. We could not find an existing License to renew. Please reach out to Illumina Customer Care to get a new license.
– If the DRAGEN server v4 is not reachable via DNS or if the Illumina License Manager service is down:
Unable to reach License Manager. Please make sure the License Manager Service is up and running.
The Custom Case Data page allows you to configure fields for case, subject, and sample information that accompanies cases in Connected Insights. The configuration covers field names, data type, restriction status, and the field category. When you upload the custom case data file, the fields in the file must be formatted to match the definition provided on this page. The information appears in the user interface on the Case Details screen and in the JSON and PDF reports in the corresponding sections.
To configure custom case data:
On the top toolbar, navigate to Configuration represented by the cog wheel icon.
Navigate to Case Data Definition.
In the right-side pane, select the Data Type from the drop-down list. This data type can be text, number, or a date. The type impacts the accepted inputs during data ingestion.
Enter a Custom Name. This name is the label that appears in the user interface and the PDF report.
Choose if you want this data to be Restricted from the drop-down list.
Select Yes if the custom case data are sensitive. When you view the Case Details, the data are hidden with asterisks as indicators, and only displays if you select Show/Hide.
If the data are non-sensitive, then select No.
Select Case, Subject, or Sample as the Associated Entity from the drop-down list. The corresponding data appears in the Case Details and on the PDF report.
Use the drag handles to change the order that data are displayed in Connected Insights and the final report.
Select Add to add the new custom case data definitions to the PDF report.
[Optional] Select the archive icon next to the custom case data definition to archive it so that it no longer appears on the final report.
[Optional] Select the X next to custom case data to remove an entry.
Custom actionability classifications can be set up in Configuration. Later, when you create therapeutic, prognostic, and diagnostic assertions, you can specify these classifications.
Create custom actionability classifications as follows.
On the top toolbar, select Configuration.
In the General tab, select Actionability Classification. The default actionability classifications are based on AMP/ASCO/CAP Li et al, 2017. If you want to specify your own, select I want to classify using my own classifications.
Provide a name for the actionability classifications (for example, ESMO ESCAT).
Select Add.
Add a classification name (eg, Level 1).
[Optional] Add a description.
Choose a color.
Select Save.
Repeat steps 4–8 until you have your classification created.
Classifications can be deleted by selecting x on the created classification.
Classifications can be edited by selecting the pencil icon on the created classification.
Use the drag handles to map your classifications to the AMP/ASCO/CAP Li et al., 2017 guideline on the right side of the window. Place your classifications in order of their significance. After you create assertions, this order is used to prioritize variants and evidence.
❗ Whenever you edit these classifications, it does not modify existing assertions in your knowledge base or reports. When you encounter assertions using older classifications, they can be edited to use the latest classification.
Before uploading samples, the lab director must create a test definition, which defines the parameters applied to samples for data processing and display.Test definitions are used to do the following:
Specify a workflow when uploading a secondary analysis result to Connected Insights.
Use the uploaded secondary analysis results to create a case.
Define parameters in the test definition associated with the workflow to apply them to the case.
The test definition defines the following information:
Supported genome builds
External knowledge bases
Applied default variant filters
Applied default variant flags
Reports available templates
Connected Insights enables user actions that are common for interpreting oncology assays data. The sequence of steps can differ between laboratories, but typically includes the following actions:
Perform the following actions during the initial setup of the software:
Configure secondary analysis data upload and sample data upload.
Configure settings (for example, QC metrics, variant interpretation, and transcripts).
Configure variant filters.
Configure the report template.
Configure the test definitions that store and automate the settings used for processing individual cases.
To review a case, perform the following actions:
Find the new case created by the data uploaded to the software.
Case flags are used at this step to assign users and categories, perform searches, and filter as needed.
On the Overview tab, review findings in key genes, genome-wide biomarkers, and key QC metrics (if configured).
On the Visualize tab, review chromosomal and other events on the Genome View plot.
On the Variants tab, review variants as follows.
Edit or create filters to customize the specific case information that displays.
Use the Integrative Genomics Viewer (IGV) to review variant quality.
Use tags to flag variants to support communication between variant reviewers.
Perform variant interpretation and include selected variants into the report as needed.
Use information from internal and external sources (for example, My Knowledge Base, JAX-CKB, and the COSMIC database) to facilitate the interpretation process. Reuse information stored for a variant that has been interpreted previously. When you remove and add variants, the draft report is automatically edited to reflect any changes.
On the Lab QC tab, review sample and variant quality information.
On the Report tab, review the draft report (if defined and enabled from the Configuration page).
Preview the final report and add the interpretation summary.
Approve the report (available only for the laboratory director role).
[Optional] Open the report and update or correct information.
The Disease Configuration section can be used to view, add, and edit the key genes associated with disease terms.
On the Configuration page, select the General tab.
Select Disease Configuration.
Select +New on the right side of the pane.
In the Disease Name field, type the disease name. This name can be based on a group of diseases or cancer types (for example, Bone).
In the Associated Disease Term(s) field, type a term (for example, Sarcoma).
Select the applicable term from the list that displays.
Make sure that the disease term displays under the field (for example, Sarcoma (SNOMEDCT: 1187396000)).
Under Key Genes, type a gene name in the field. You can enter one gene name per line, or multiple gene names separated by commas. A maximum of 250 names can be entered. The names are case-sensitive.
Select Save.
On the Configuration page, select the General tab.
Select Disease Configuration to expand the list of disease categories.
Select a disease (for example, Bone).
On the right side of the screen, select Edit.
Update the disease terms as follows. a. To add a disease term, type the term (for example, Sarcoma) in the Associated Disease Term(s) field. b. Select the applicable term from the list that displays. c. Make sure that the disease term displays under the field (for example, Sarcoma (SNOMEDCT: 1187396000)). d. To delete a disease term, select the X next to it. e. Select Save to accept any changes.
Update the key gene names as follows. a. For Key Genes, enter a gene name in the field. You can enter one gene symbol per line, or multiple gene names separated by commas. A maximum of 250 names can be entered. The names are case-sensitive. b. Select Save to accept any changes.
Update genome wide thresholds as follows. a. For Genome Wide Thresholds, enter values for the following Tumor Mutational Burden (mut/MB) thresholds:
TMB-Low (the range starting point defaults to 0.0)
TMB-High
❗ If there is a conflict between the low and high values, an error message displays indicating which value needs to be corrected.
b. Enter values for the following Microsatellite Instability (% unstable sites) thresholds:
MS-Stable (the range starting point defaults to 0.0)
MSI-High (the range end point defaults to 100)
c. Enter values for the following Global Instability Score thresholds:
GIS-Low (the range starting point defaults to 0.0)
GIS-High
d. Select Save to accept any changes.
The following table shows the default key genes for select cancer types based on data provided by the Illumina Medical Affairs team:
On the Configuration page, select the General tab.
Select Disease Configuration.
Select ....
Select Restore to Default.
To confirm the action, select Yes,Restore to Default.
To confirm the action, select Yes, Delete.
Illumina Connected Insights is a software solution that enables tertiary analysis of next-generation sequencing (NGS) data. There are two versions of Illumina Connected Insights:
Connected Insights - Cloud—This version is hosted by Illumina.
Connected Insights - Local—This version is installed on the local DRAGEN server v4. Both versions of Illumina Connected Insights have the same functionality, but Connected Insights - Local has differences in installation, administration, and license management due to the method of deployment.
In the current version, Connected Insights enables tertiary analysis of variant data generated using somatic oncology assays. The software accepts data generated from DNA and RNA sequencing workflows and can be configured to accept input data from oncology assays and variant callers. Connected Insights integrates several genomic databases that are used to annotate uploaded data to help understand its biological significance.
The software supports variants frequently identified in tumor samples (for example, SNVs, insertions, deletions, fusions, and structural variants). The software also accepts and enables user interpretation for genome-wide biomarkers (for example, tumor mutational burden (TMB), microsatellite instability (MSI), and genomic instability score (GIS) used to assess homologous recombination deficiency (HRD)).
The software has the following features:
Automated upload of secondary analysis files and case creation
Case management
Annotation of genes and variants using connected databases
Storage of variant interpretation records (assertions) produced by the user
Configurable test definitions
Customizable gene and variant filters
Visualization of variant information
Generation and editing of summary reports
The following illustration shows typical data flow in Connected Insights - Local
Below is illustration of network interaction of Connected Insights - Local
Before installing the Connected Insights - Local software, review and complete the prerequisites. For instructions, refer to .
Once the prerequisites are met, complete the installation of Connected Insights - Local software in the sequence below:
Download the Connected Insights - Local software packages. For instructions refer to
Install the Connected Insights - Local software. For instructions, refer to
Install the Connected Insights - Local software license file. For instructions, refer to
Sign in to Connected Insights - Local software. For instructions, refer to
Configure external storage. For instructions, refer to
Install Annotations, Genome Data Reference and Knowledge Bases packages from Software updates page. For instructions, refer to section Install or Update software and dependent package.
Upload License quota file from Software updates page. For instructions, refer to section Update License (ConnectedInsights-QuotaLicense.bin) from Local Computer.
After completing the above instructions to install Connected Insights - Local software, follow the instructions in to set up Connected Insights - Local software and to ingest cases from secondary analysis data.
Before starting the installation or update of Connected Insights - Local software, make sure that the following prerequisites are met.
Ensure the DRAGEN Server v4 configuration is as below:
DRAGEN server v4 with Oracle Linux 8. The preferred version of Oracle Linux 8 is preinstalled on the DRAGEN server v4. The DRAGEN server v4 software pipeline is also included.
DRAGEN server v4 setup shall be completed following the Illumina DRAGEN Server v4 Installation Guide (document #200015717). For more information, refer to Illumina DRAGEN Server v4 Installation Guide on the .
DRAGEN server v4 is idle during installation or update of Illumina Connected Insights - Local software.
If you are setting the hostname for a DRAGEN server v4, ensure the server has FQDN (Fully Qualified Domain Name) (Example: If the server's hostname is onpremtest and domain is abcd.com, then the server shall be registered as onpremtest.abcd.com in your organization's DNS(Domain Name Server)). If your organization does not have a DNS server, then ensure to setup the server with a static IP and the /etc/resolv.conf file shall be an empty file with no contents in it. Once set up, this configuration will be required for installation and cannot be changed throughout the software's usage. If it changes in the between, then application may not behave as intended and could possibly throw errors. Thus, ensure to finalize the configuration i.e. with FQDN (Or) with Static IP before starting the installation process mentioned in this document.
You must have root or sudo privileges to run installation commands. To access the DRAGEN server v4 and run commands from the command-line interface, you should be familiar with the Linux commands used to install the software and config file (in case of upgrade from current installed version to the new version).
An external storage drive must be connected to the DRAGEN server v4 directly or through the network. If an external storage drive meeting the requirements below is not mounted already, refer to the section for details on how to mount an external storage drive.
Below are the minimum requirements of the external storage which shall be mounted on the DRAGEN server v4.
Configured with CIFS/SMB or NFS protocols only. Recommended to use NFS v3.5 and above or CIFS/SMB v3.1 and above protocol for data security. Illumina also recommends an encrypted data storage drive to safeguard your data.
100 gigabytes (GB) of available storage space.
Recommended: 10 Gb (Gigabits) per second of network speed.
The external storage drive is used by Connected Insights - Local software to read inputs and write outputs.
For inputs, Connected Insights - Local software reads secondary analysis data (for example, VCF and BAM files).
For outputs, Connected Insights - Local software writes analysis output data and backup files (for example, annotated VCF files, visualization files, and PDF report files).
In Illumina's welcome email or customer notification email, all the links to download the packages shall be accessible. If you are unable to reach to any of the sites, please check with your IT to whitelist the URLs. The example URLs are https://support.illumina.com/downloads/* and https://illumina-use1-ici-local-release-data.s3.amazonaws.com/releases/knowledgebases/*
A personal computer which has a remote access client tool to connect to the DRAGEN server v4 to run the commands and a browser to access Connected Insights - Local software application after software is installed.
Below are the mandatory packages needed to install Illumina Connected Insights - Local software.
Connected Insights Packages — The files are downloaded from the using Downloader Utility.
Illumina Connected Insights - Local software: This is the base software package. File size: ~14 GB; file extension: .run
Illumina Connected Annotations: This is the Annotations sources package. File size: ~90 GB; file extension: .run
Illumina Connected Genome Data Reference: This is Genome references and visualization package. File size: ~11 GB; file extension: .run
Connected Insights - Local software license files — These are 2 files provided to the customers by Illumina via email. Both need to be downloaded to your personal computer. One License file (ConnectedInsights-Local-SetupLicense.bin) is required to access the Connected Insights - Local software application before signing into the application and the other License File (ConnectedInsights-Local-QuotaLicense.bin) is required to add Genomic Equivalent (GE) sample credits required to perform tertiary analysis (Process Cases). Both files are mandatory to be installed.
Knowledge Base files — These files are downloadable from the links provided by Illumina. Please contact connectedinsightslocal@illumina.com to receive the links.
JAX-CKB (File extension: .run)
CIViC (File extension: .run)
OncoKB (File extension: .run)
❗ To avoid errors during installation, make sure to not alter the names or the extensions of the downloaded files and all the files shall have execute permissions.
For downloading the packages listed in point 1, use the software Downloader Utility compatible to your download environment (Mac, Windows or Linux) from the . The utility shows the progress of the current package being downloaded and exits out of the terminal once downloading all the packages completes.
If the download was interrupted, the Downloader Utility can be re-executed by providing the same file path which will resume the download from where it paused previously.
There are 3 different ways to make the Connected Insights - Local software packages accessible on the DRAGEN v4 server. You can use any one of the below options to download and make the files accessible.
❗ Downloading all the packages on an average network speed of 300 Mbps takes between 8 to 10 hours. Downloading all the packages on the recommended network speed of 10 Gbps takes 1 to 2 hours.
❗ For Linux, we currently support only Oracle Linux 8 (glibc version≥2.28 and x64), which is the base operating system installed on the DRAGEN server v4. This utility is tested only on the DRAGEN server v4 with Oracle 8 and not other flavors of Linux.
Login to the DRAGEN server v4 via root or a user with sudo permissions and navigate to the /staging
folder: cd /staging
Download the Downloader Utility
Once you click on the utility, you will be redirected to Illumina account page. Enter your valid Illumina account details. Upon successful login, when prompted, enter either your Customer Number associated with your MyIllumina Account (Or) the valid DRAGEN server v4 serial number. To get the DRAGEN server v4 serial number, login to the DRAGEN server v4 using the root or sudoer user and enter one of the following commands on the DRAGEN server v4: dragen_lic | grep Board
or dragen_info -b | grep Serial
. Copy the string after SN and enter it in the box prompted on the browser. This begins to download the utility which is ~8 to 10 MB in size.
Once it validates, it will generate a presigned URL which is valid only for sometime. Copy this pre-signed URL if you want to directly download the files to the DRAGEN server v4 and on the command prompt enter wget "<CopiedPresignedURL>" -O ici_downloader_unix
(Or) you can also download this utility on your laptop/computer and then secure copy (scp command) the utility to the DRAGEN server v4.
Once downloaded, make sure the Downloader Utility has execute permission: chmod +x ici_downloader_unix
Run the Downloader Utility: ./ici_downloader_unix
When prompted to Please enter the path
, enter: /staging
. This will create the folder /icipackages
under /staging
and download all the Connected Insights Packages files from the support site to there.
Once the Downloader Utility completes downloading, copy the Knowledge Base files (JAX-CKB, CIViC and OncoKB) received from the email link into the /icipackages
folder.
Make sure all the files have execute permissions. Execute these 2 commands:
cd /staging/icipackages
chmod +x "illumina_connected_insights_<JAX-CKB file name suffix>.run" "illumina_connected_insights_<CIViC file name suffix>.run" "illumina_connected_insights_<OncoKB file name suffix>.run"
❗ For Linux, we currently support only Oracle Linux 8 (glibc version≥2.28 and x64), which is the base operating system installed on the DRAGEN server v4. Refer to the above section.
(Or)
You will be redirected to Illumina login page. Enter your valid Illumina account details. Upon successful login, when prompted enter with your Customer Number associated with your MyIllumina Account (Or) the valid DRAGEN server v4 serial number. To get the DRAGEN server v4 serial number, login to the DRAGEN server v4 via root user and on the command prompt enter one of these commands: dragen_lic | grep Board
or dragen_info -b | grep Serial
. Copy the string after SN and enter it in the box prompted on the browser. Upon success, choose a location to download the utility which is about ~11 to 12MB in size.
Once downloaded, make sure the Downloader Utility has execute permissions.
For MacOS (11.0 arm64 or higher), execute this command within the folder containing the Downloader Utility file:
chmod +x ici_downloader_mac
For WindowsOS (Win11(x64) or higher), in File Browser, right click the Downloader Utility file, click Properties, then go to Security. Confirm the groups and users have all permissions in the Allow column ("Special permissions" not required). To add permissions, click Edit....
Run the Downloader Utility.
For Macos (11.0 arm64 or higher), execute this command from the folder containing the Downloader Utility file:
./ici_downloader_mac
For WindowsOS (Win11(x64) or higher), double click on the executable (or) open Windows Command Prompt and execute the below command from the folder containing the Downloader Utility file:
.\ici_downloader_windows.exe
When prompted, enter the absolute file path to the mounted external storage drive directory where you want to download all the software packages.
Examples:
For MacOS (11.0 arm64 or higher): /Volumes/<Root directory of mounted external storage drive>
For WindowsOS (Win11(x64) or higher): \\<Root directory of mounted external storage drive>
This will create a folder called icipackages
under the directory <Root directory of mounted external storage drive>
and downloads all the software files from the support site to there. Once the download completes successfully, the Downloader Utility will exit out of the terminal.
Once the Downloader Utility completes downloading, copy the Knowledge Base files (JAX-CKB, CIViC and OncoKB) received from the email link into the icipackages
folder.
Make sure all the files have execute permissions.
For MacOS (11.0 arm64 or higher), execute this command in the icipackages
directory:
chmod +x "illumina_connected_insights_<JAX-CKB file name suffix>.run" "illumina_connected_insights_<CIViC file name suffix>.run" "illumina_connected_insights_<OncoKB file name suffix>.run"
For WindowsOS (Win11(x64) or higher), the files may have execute permissions by default. To confirm or edit, see step 4 above.
(Or)
Use this download method when the DRAGEN server v4 is not connected to the internet, incapable of having a personal laptop mount to it, or if the software files cannot be made available on the DRAGEN server v4 via the two methods above for other reasons.
The USB drive must meet the following requirements:
USB 3.0
At least 150 GB of storage space to accomodate all the files
xfs or ext4 format file system
Download the files via the USB method as follows:
Download and execute the Downloader Utility on your laptop by following steps 2-5 in the section above ("Download to external storage drive mounted on the DRAGEN server v4 using your personal computer").
Unplug the USB from your laptop. Take the USB and insert it into the DRAGEN v4 Server.
Login to the DRAGEN v4 server as root or sudo user and create a folder named /usbinstall
under the /media
folder with the following command: mkdir -p /media/usbinstall
Run the following command to mount the connected USB drive partition that contains the downloaded Connected Insights Packages files and Knowledge Base files to the DRAGEN server v4:
mount /<path to USB partition with downloaded files> /media/usbinstall
Run the following commands to make sure that the downloaded files have executable permissions:
cd /media/usbinstall
chmod +x *
After the license installation, once you are redirected to this Login page, using the following default login information to create the first-time administrator account:
Username —icidefault
Password — P@ssw0rd@123
After you sign in, you must add an administrator user. Populate the following fields:
Username
First Name
Last Name
Email Address
Create Temporary Password
Confirm Password
Select Save.
A page displays indicating that the default account has been suspended and that you can sign in under your administrator username. Select Continue. This will take you to the login page.
Using your administrator username and temporary password, sign in to Connected Insights - Local software.
After reading the Master Service Subscription Agreement (MSSA), select I Accept.
Enter a new password in the New Password and Confirm Password fields and select Reset.
Select your security questions and select Save. After you save, you will be logged off.
Now sign in to the application with your administrator username and password.
Upon successful sign in, you will see 3 notifications. These notifications will continue to display until Installation steps 5 and 6 from Introduction - Software Installation (New Customers), Step 5 (Configure external storage. For instructions, refer to ) and Step 6 (Install Annotations, Genome Data Reference and Knowledge Bases packages from Software updates page. For instructions, refer to ) are completed.
Your Genome Equivalent Sample balance has reached 0. Case ingestion has been stopped. Please contact administrator or Illumina Sales team.
External storage drive has not been setup. Go to Administration Console -> Storage drives to configure.
One or more required packages are not installed. Go to Administration Console -> Software Update to install.
❗Note: Illumina recommends having at least two users with Administrator privileges to prevent any potential lockout from the Administrator user login when managing actions on the Administration Console.
The Connected Insights - Local software installation process can take approximately 45–60 minutes based on network speed.
Login to DRAGEN server v4 via root or sudoer user and navigate to the directory where you made the installation files accessible to the DRAGEN server v4. This directory depends on how you downloaded and made the files accessible to the DRAGEN server v4 (as instructed by the section ).
If you downloaded directly to DRAGEN server v4 connected to internet, use the command:
cd /staging/icipackages
If you downloaded to the external storage drive mounted on the DRAGEN server v4 using your personal computer, use the command:
cd /mnt/<Path to the directory that the storage drive is mounted to>/icipackages
If you downloaded and copied the files to a USB drive, use the command:
cd /media/usbinstall
Note: you are in the correct directory if the command ls
returns all of the installation files you downloaded.
Start installation:
nohup ./illumina_connected_insights_local_<version>.run &
Note: Replace <version>
with the version number in the file name (e.g., 5.0.0
). If desired, you may replace ./
with the absolute file path (e.g., nohup /mnt/ici_mount/icipackages/illumina_connected_insights_local_5.0.0.run &
).
After running the command, press Enter.
Run the following command to monitor the progress:
tail -f nohup.out
Wait for a success or failure/error message to display in the command prompt and in the log file (nohup.out). This may take 45-60 minutes. Examples of the success and failure messages and next steps are below.
If the installation is successful, the following 2 messages will display in the command prompt and the log file (nohup.out):
Success message: Success: Illumina Connected Insights software installation is successful.
URL message: The software generates the URL you can use to access the application via a web browser. There are two forms of this message based on the DNS configuration of the DRAGEN server v4:
If the DRAGEN server v4 is configured with a fully qualified Domain Name:
Info: Illumina Connected Insights software application can be accessed at https://<FullyQualifiedDomainName>/login
If the DRAGEN server v4 is configured with a Static IP address:
Info: Illumina Connected Insights software application can be accessed at https://<IP address>/login
❗ Ensure you access the application using the URL printed in nohup.out otherwise it might throw blank errors after the page loads.
If you receive a browser message indicating that your connection is not private, disregard and proceed to the URL. This is normal and does not impact anything.
Note: After the installation is successful, Connected Insights - Local software creates the following on the DRAGEN server v4:
/staging/ici_analysis_dir
This directory will be deleted after the External Storage drive is configured and the data stored here is moved to external storage drive.
/staging/ici
/staging/ici_temp
/var/log/
❗ Do not delete or alter content in these folders or files. If the files are deleted, new cases cannot be processed, or case results may not be available. If the contents of /var/log are deleted, then we will lose the files needed for troubleshooting in case of any failures.
The Preferred Transcripts section allows you to upload a preferred transcript file that defines which transcripts for a gene are preferred. These transcripts are prioritized over other transcripts of the gene when the default transcript for a variant is determined. For more information, refer to .
Upload the preferred transcript file as follows.
On the top toolbar, select Configuration, and then select the General tab.
Select Preferred Transcripts.
If there are no preferred transcripts, select Create One.
For Template File, select Upload and select your transcript file. You can also download a template to customize and upload as your preferred transcript file.
Select Open.
After the file displays, Select Save.
Select Download & View to download the transcript file.
[Optional] To upload an updated version of the file, select Upload New Version.
The following illustration shows typical user actions in Connected Insights.
On the Chrome Browser launch , select View Options and then Download Utility - Unix (compatible with DRAGEN server v4).
This completes the downloading step. Proceed to installing the software by following the instructions in .
Make sure the personal computer is mounted to the external storage drive directory. Also make sure that external storage drive directory is mounted to the DRAGEN server v4 as well. For details on how to mount the external storage to your laptop, refer to .
Download the Downloader Utility from , select View Options and choose either Download Utility - Windows or Download Utility - Mac based on what is compatible with your download environment operating system (Mac or Windows)
This completes the downloading step. Proceed to installing the software by following the instructions in .
From your laptop which has access to the links to download all the mandatory packages, format the USB with the partition/label name as usbinstall. For instruction on how to format a USB, refer to section "Prepare USB compatible with DRAGEN v4 server (type xfs or ext4 only)".
When prompted, enter the absolute file path to either the usbinstall folder to download directly to the USB (Or) the file path to a folder on your laptop and then copy the files to the usbinstall folder once downloading completes. Once the Connected Insights Packages files are completely downloaded on/copied to usbinstall, copy the Knowledge Base files (JAX-CKB, CIViC and OncoKB) received from the email link into the usbinstall folder. For instructions on how to copy files to the USB, refer to under the same section "Prepare USB compatible with DRAGEN v4 server (type xfs or ext4 only)".
This completes the downloading step. Proceed to installing the software by following the instructions in .
Click on the Administration Console -> Storage Drives to complete the Step 5 of Installation steps from Introduction - Software Installation (New Customers). You will be redirected to configure
On your laptop, open a browser and enter the URL to access the Connected Insights - Local software application to perform the remaining steps by proceeding to .
If the installation fails or an error occurs, a message displays that provides information on how to resolve the error. For more information, refer to . If you must reinstall, refer to .
Field Name | Description |
Cancer Types | Key Genes |
Melanoma | BRAF, KIT, NRAS, NTRK1, NTRK2, NTRK3, TERT, GNAQ, GNA11, BAP1, SF3B1, EIF1AX,CDKN2A, BRCA2, PALB2, NF1, PTEN, CDK4, MC1R, MITF, MBD4 |
Prostate | ATM, BARD1, BRCA1, BRCA2, BRIP1, CDK12, CHEK2, FANCL, FGFR2, FGFR3, PALB2, PPP2R2A,RAD51B, RAD51C, RAD51D, RAD54L, NTRK1, NTRK2, NTRK3, ATR, EPCAM, ABRAXAS1,FANCA, GEN1, MLH1, MRE11, MSH2, MSH6, MUTYH, NBN, PMS2 |
Uterine and Cervical | ERBB2, ESR1, FOXO1, NCOA3, PAX3, PAX7, SMARCA4, SUZ12, NTRK1, NTRK2, NTRK3, ALK,ATRX, BCOR, CDK4, DICER1, FGFR2, GREB1, KMT2C, MDM2, MYBL1, NCOA2, CD274, PGR,PHF1, PIK3CA, PLAG1, RAD51B, RB1, TERT, TFE3, TP53, YWHAE, PTEN, POLE, MLH1, MSH2,MSH6, PMS2 |
Lung | ALK, BRAF, EGFR, ERBB2, KRAS, MET, NUTM1, RET, ROS1, NTRK1, NTRK2, NTRK3, CD274 |
Breast | BRCA1, BRCA2, ERBB2, ESR1, PIK3CA, NTRK1, NTRK2, NTRK3, CD274, PALB2, RAD51D,RAD51C, ATM, STK11, TP53, NF1, NBN, PTEN |
Thyroid | BRAF, HRAS, KRAS, NRAS, RET, TERT, NTRK1, NTRK2, NTRK3, PAX8, PPARG, PTEN |
Ovarian | BRCA1, BRCA2, FOXL2, NTRK1, NTRK2, NTRK3, ATM, BRIP1, MLH1, MSH2, PALB2, RAD51C,RAD51D, NBN, STK11 |
Colorectal | BRAF, ERBB2, KRAS, NRAS, NTRK1, NTRK2, NTRK3, MLH1, MSH2, MSH6, PMS2 |
CNS | ATRX, BRAF, EGFR, H3F3A, HIST1H3B, IDH1, IDH2, PTCH1, TERT, TP53, NTRK1, NTRK2,NTRK3, MGMT, PTEN |
Bone | EWSR1, EGFR, ERG, ETV1, ETV4, FLI1, IDH1, NTRK1, NTRK2, NTRK3, FEV, IDH2, FUS |
Other Solid (as a default for any other cancertypes) | ALK, APC, BCOR, BRAF, BRCA1, BRCA2, CDK4, CIC, CTNNB1, DNAJB1, ERBB2, EPCAM, ERG,ETV1, ETV4, ETV6, EWSR1, FGFR2, FGFR3, FOXO3, GLI1, IDH1, KIT, KRAS, MDM2, MLH1,MSH2, MSH6, MYOD1, NAB2, NTRK1, NTRK2, NTRK3, PAX3, PAX7, PDGFRA, PMS2, RANBP2,SDHB, SMARCB1, TFE3, WT1, YAP1, RET, ROS1, MET, IDH2 |
User-defined automation can add assertions from your knowledge base and/or other knowledge bases automatically to a draft report.
Automation only applies to cases using a test definitions with automation turned on during case ingestion. Cases that were ingested before automation was turned on will not have assertions automatically added to their reports.
Automated assertions can be added for all types of variants with assertions in the supported knowledge bases, including the genome-wide biomarkers TMB, MSI, and GIS. Automation configuration settings determine which biomarkers are included in automation and which assertions for those biomarkers are added to the report.
You can also edit or remove assertions that were automatically added before approving a report. For more information, refer to Edit, Remove, and Archive Assertions.
Before enabling automation, make sure that the following information is set up:
Key genes and TMB, MSI, and GIS thresholds to limit reporting to certain biomarker scores. For more information, refer to Disease Configuration.
Preferred transcripts to limit reporting to preferred transcripts. For more information, refer to Preferred Transcripts.
Default filters to limit the variants being reported. For more information on creating variant filters and adding them as default filters in a test definition, refer to Variant Filters and Test Definition Setup.
Select either of the following sets of variants to be reported:
Variants that appear in a default filter and key genes (i.e., Key Findings of the Overview page).
Variants that appear in a default filter.
The following are not reported:
Any variant with a likely benign, benign, or likely neutral biological classification in a knowledge base (including My Knowledge Base and ClinVar).
Any variant with no biological classification in any knowledge base (including My Knowledge Base and ClinVar), and biological classification predicted by the Oncogenicity Prediction tool is VUS, likely benign, or benign.
TMB, MSI, and GIS with an unknown status.
Max number of variants eligible for reporting:
If variant selection is Variants that appear in default filter and key genes, only the first 70 variants with assertions in your default filters that are in key genes are eligible for reporting.
If variant selection is Variants that appear in default filter, only the first 70 variants with assertions in your default filters are eligible for reporting.
You can select KBs you want to report assertions from. The following KBs are selectable:
My Knowledge Base
JAX-CKB
CIViC
OncoKB
You can also reorder KBs to prioritize assertions. Select and hold the icon to the left of the KB and move it up or down to reorder the KB list. Connected Insights uses the following information to prioritize which KB is used to report findings:
Order in the KB list (for example, if you move My Knowledge Base above JAX-CKB in the KB list, then My Knowledge Base is prioritized)
Case disease and assertion disease match (for example, if JAX-CKB is below My Knowledge Base in the KB list, but the case disease matches the JAX-CKB assertion disease, then JAX-CKB is prioritized)
On the Configuration page, select the General tab.
Select Report Automation, and then select Edit.
Select one of the following Report a biomarker when options:
Appears in a default filter and Key Genes (Key Findings)
Appears in a default filter
Select applicable knowledge sources from the following Report findings from options:
My Knowledge Base
JAX-CKB
CIViC
OncoKB For more information, refer to Knowledge Base Selection. After making your selections, a window displays indicating the reporting status for each classification.
Select Yes or No for the following questions:
Report assertions previously reported only?
Report therapeutic assertions with highest classification only, skipping anything in a lower classification?
Report therapeutic assertions that indicate response or resistance only?
Select Save.
Turn on automation within a test definition. For more information, refer to Test Definition Setup.
Test Definitions allow you to specify default parameters that apply to cases when they are ingested. Make sure you have test components created, then create a test definition as follows.
On the top toolbar, select Configuration.
Select the Test Definitions tab.
Select New.
In the right-hand pane, enter a test name in the Test Name field.
Choose a human reference genome.
[Optional] Select one or more custom annotations (must be compatible for the selected human reference genome).
Choose one or more variant filters. These filters display in the Case screen as locked filters.
Choose a variant flag group.
Choose a report template from the Report Template drop-down list.
[Optional] Enter version comments as applicable.
[Optional] Select the Turn on Automation toggle to enable or disable the automated addition of assertions to reports using this test definition. For more information, refer to Automation.
Select Save. The new test definition appears on the left-hand accordion menu. Select a test definition to preview and access the following actions:
Select Edit to edit a test definition.
Select Copy as New Test to copy the definition as a template for a new test definition.
Select Archive to hide the test definition from the PDF report.
Configure the pipeline metrics that appear on the report and edit the default values for each metric as follows.
On the top toolbar, select Configuration, and then select the General tab.
In the left-side pane, select Pipeline & QC Configuration.
Select the applicable pipeline. QC metric configurations display to the right of the selection.
Select Edit.
To add or remove metrics from the report, select the Add to Overview & Report toggle for each metric.
To edit specification limits for applicable metrics, select the Lower Spec Limit or Upper Spec Limit fields and enter the new value. If you cannot edit a value, NA replaces the field.
[Optional] To undo all of your changes, select Reset to Default Values.
Select Save. The updated metrics appear in the Lab QC tab of the case along with the Pass/Fail designations.
In Connected Insights, use the default report template or introduce customizations to configure the reports according to your specifications. For more information on using the default report template, refer to Report Templates.
The following applications can be used to customize the report:
LibreOffice v7.5 or later
Carbone Studio Illumina recommends using LibreOffice to customize the report. For more information on the customizations that can be done with LibreOffice, refer to the writer guide on the LibreOffice website. Carbone studio and its documentation are updated regularly. Please ensure any command used in an ODT is compatible with Carbone version 4.22.4 or earlier.
Use LibreOffice or an equivalent ODT editor to do common report customizations, including:
Changing the logo in the header.
Changing the report name.
Updating the date and time format.
Adjusting the font size and color.
Reordering and removing sections.
Inserting or removing information, such as single or aggregate data and the Genomic biomarkers table asterisk.
Changing the paper size.
Update Methodology Description and Gene List.
Show Findings by Tier
Prepare the image file that is going to be inserted into the template.
Make sure that the image is between 200 and 600 pixels so that it can fit within the header.
Make sure that the image file size is less than 50 KB to avoid a delay in report generation.
Open the template in the ODT editor.
Replace the Laboratory image in the header as follows. a. Select the Laboratory image within the header of the first page. b. Replace the image with the formatted image from step 1. If you are using LibreOffice, right-click and select Replace. For more information on LibreOffice functions, refer to the writer guide on the LibreOffice website. The location and size are adjustable after the image is placed in the header.
❗ The default template includes a different header style for the first page and subsequent pages.
c. Select the image in the header of the second page. d. Replace the image with the formatted image from step1. If you are using LibreOffice, right-click and select Replace.
For more information on LibreOffice functions, refer to the writer guide on the LibreOffice website. This replacement causes the header image to change in subsequent pages.
Open the template in the ODT editor.
At the top of the template of the first page, replace the following text with the new report name: {d.reportData.reportLabels.report:ifEM():show('Report'):upperCase()}
❗ The default template includes different report name text for the first page and subsequent pages.
Repeat step 2 for the second page. This replacement causes the report name to change in subsequent pages.
Open the template in the ODT editor.
At the top of the template, find the following code that generates the report updated time text: {d.subjects[0].reports[0].reportDetails.updateDate:formatD('YYYY-MM-DD HH:mm')}
Replace YYYY-MM-DD HH:mm
with the desired format (for example,YYYY-MM-DD
).
Open the template in the ODT editor.
Find and replace every instance of (UTC)
with {d.reportData.localDates.timezone.shortName}
. This will replace "UTC" with the local time zone abbreviated name (for example, "PT" for Pacific Time).
Find the following code that generates the updated date and time text: d.subjects[0].reports[0].reportDetails.updateDate
Replace every instance with d.reportData.localDates.reportUpdateDate
Find the following code that generates the report approval date and time text: d.reportData.reportHistory[i].approvedDate
Replace every instance with d.reportData.reportHistory[i].approvedDateLocal
Open the template in the ODT editor.
Change the font color and style using the font characteristics function for an individual text section.
❗ Color and size are changeable, but the font style and type cannot be altered.
[Optional] If you must update the font color and size for the whole document, adjust the paragraph style.
Open template in the ODT editor.
Identify the sections that must be rearranged.
Select and copy all relevant text or tables in that section.
❗ The sections of the template primarily consist of tables. Make sure that the entire table is selected when reordering a section. If you do not,then formatting issues can occur.
Enter a paragraph break between the sections where the copied section is being placed.
Paste the copied section to the new location.
Make sure that all of the information is present and formatted correctly.
Delete the original section.
Repeat steps 1–7 for any other sections that must be reordered.
Open the template in the ODT editor.
Select the section of the report that you want to remove.
❗ The sections of the template primarily consist of tables. To remove the section, make sure that the entire table is selected. If you do not, then formatting issues can occur.
Delete the section.
Insert single data (for example, Methodology) or aggregate data as follows.
Open the template in the ODT editor.
Place the cursor where you want the new information to appear.
Add the applicable code or text used to generate new content or enter free text that you want to appear in all of the generated reports. For example, enter {d.createdDate:formatD('YYYY-MM-DD')}
for the date the report was created or {d.reportData.therapies[]:aggCount}
to add a count for the number of therapy assertions included in the report.
Open the template (version 1) in the ODT editor.
Search for and delete the following line (use Ctrl+F to search): {$lbl.gbTableFooter:ifEM():show('*Contains disease related genes only')}
Search for the following and delete only the asterisk (*
): ('Nothing reported')}*
Open the template (version 2) in the ODT editor.
Search for the following line (use Ctrl+F to search): {$lbl.nothingReportedV2:ifEM():show('Nothing Reported')}
Use the ODT editor delete the table row containing the searched for text above.
Open the template in the ODT editor.
Search for supplemental information in the search field at the bottom of the template. You can also select Ctrl+F to search.
Make the desired edits. For more information on complex edits, refer to the ODT editor help documentation. The following edits are common:
Change an existing term heading or its definition by updating the text within the single quotation marks for a given term or definition. For example, {$lbl.geneList:ifEM():show('Gene List')}
can be changed to the following: {$lbl.geneList:ifEM():show('Genes Included In This Test')}
Add static text (for example, laboratory contact information) by placing the cursor outside of the braces ({ })
where the status text begins. Then, type the text. If needed, press Enter to start a new line. Refer to the following example:
Before editing:
{d.dataSourceVersions}{d.dataSourceVersions:ifEM():showBegin()}{$lbl.notProvided:ifEM():show('Not provided')}{d.dataSourceVersions :showEnd()}
After editing:
{d.dataSourceVersions}{d.dataSourceVersions:ifEM():showBegin()}{$lbl.notProvided:ifEM():show('Not provided')}{d.dataSourceVersions :showEnd()} Contact Information Name of Laboratory +1 (123) 555-1234 Email@Email.com
Open the template in the ODT editor.
Select each paragraph style and adjust the page size to the required size needed for printing.
Open the template in the ODT editor.
Search for and delete the following line (use Ctrl+F to search):{d.reportData.methodology.assayDescription:convCRLF()}
Replace line with desired methodology text used for the specified workflow. Example text can be found in the default PDF generated from a case in ICI.
Search for and delete the following line (use Ctrl+F to search):{d.reportData.methodology.assayGeneListText:convCRLF()}
Replace line with desired gene list.
The version 2 template can conditionally display findings at the beginning of the report based on the Tier/Actionability level. The default shows all levels in this section. To only display Tier I and Tier II (or equivalent).
Open the template in the ODT editor.
Search for the following line (use Ctrl+F to search):classification.actionabilityOrder:ifGTE(7.0)
Change 7.0 to 5.0 in the instances of the line.
Search for the following line (use Ctrl+F to search):classification.actionabilityOrder>6.9999
Change 6.9999 to 4.9999 in all instances of the line.
Use APIs to perform the following tasks in Connected Insights:
Get the case ID
Add or update the disease for a case
Search cases
Delete cases
Upload Case Metadata files
❗Do not use the Update Case Information or Patch Case APIs. These APIs can significantly alter case data and are only used by Illumina TechnicalSupport.
On the API page, navigate to the Cases section.
Select GET /crs/api/v2/cases/{caseId}.
In the Parameters table, update the description for the following required parameters:
caseId — The ID for the case. To retrieve this ID, select the applicable case in Connected Insights and copy the ID from the URL (for example, https://{domain}.connectedinsights.illumina.com/interpretation/{caseId}/reports/{reportId}/overview
).
directIdentifiers — This parameter includes or ignores direct identifiers. Select true or false from the drop-down list. The default value is false.
includeQcOverviewMetrics — This parameter includes or ignores the QC metrics for the case. Select true or false from the drop-down list. The default value is false.
Accept-Language — The applicable language for the data.
Select Execute.
On the API page, navigate to the Cases section.
Select PUT /crs/api/v1/cases/{caseId}/diseases.
❗ This API puts the case in a processing state. Then, it moves to the Ready for Interpretation state. Navigate to the Case List page to check the status of the case.
In the Parameters table, update the description for the following parameters:
caseId — The ID for the case. To retrieve this ID, select the applicable case in Connected Insights and copy the ID from the URL (for example, https://{domain}.connectedinsights.illumina.com/interpretation/{caseId}/reports/{reportId}/overview
).
For the Request body, enter the disease name you want to add or update. Refer to the following example:
{
"externalid": "255032005",
"ontologytype": "SNOMEDCT",
"name": "Medullary thyroid carcinoma"
}
Select Execute.
Use an API to delete cases as follows.
On the API page, navigate to the Cases section.
Select DELETE /crs/api/v1/cases/{id}
In the Parameters table, enter the applicable case ID.
[Optional] Enter the applicable language in the Description field.
Select Execute.
Use an API to search for cases based on one or multiple parameters. If you are using multiple parameters, the search is completed with the AND condition for each parameter.
On the API page, navigate to the Cases section.
Select GET /crs/api/v1/cases/search.
In the Parameters table, update the description for the following applicable parameters:
status — The case status. Enter the applicable status in the field. The available statuses are listed in the Description column.
isExactMatch — This parameter is used with displayId and determines if the result is an exact match. Select true or false from the drop-down list. The default value is false.
displayId — The displayed case ID ( for example, ILM-ABC-234 ). This parameter is an exact search when isExactMatch is set to true.
id — The caseId ( for example, dc25cd92-78e0-11e8-adc0-fa7ae01bbebc ). This parameter is also used to search for a partial ID.For example, if you search for 11e8, then dc25cd92-78e0-11e8-adc0-fa7ae01bbebc displays in the results.
externalSampleId — The external sample ID for a case ( for example, ILM-ABC-234 ). This parameter is also used to search for a partial ID. For example, if you search ABC or 234, then ILM-ABC-234 displays in the results.
analysisId — The specific or custom analysisId.
tags — The tags associated with the case. Select Add string item to add a tag. This parameter is also used to search for partial tags. For example, if you search for onc, then both oncogenic and oncology display in the results.
diseaseName — The disease name associated with the case.
creationDateBefore — The date before the data is created. This date is in the yyyy-MM-dd'T'HH:mm:ss'Z' format ( for example,2021-01-30T08:30:00Z ).
creationDateAfter — The date after the data is created. This date is in the yyyy-MM-dd'T'HH:mm:ss'Z' format ( for example, 2021-01-30T08:30:00Z ).
pageNumber — The specific page number of the API response.
pageSize — The size of each page in the API response.
orderBy — This parameter is used by id, displayId, and status to sort results. Results are sorted in ascending or descending order.Enter ASC to sort in ascending order, and enter DESC for descending order.
Accept-Language — The applicable language for the data.
Select Execute.
Use an API to upload a Case Metadata file as follows.
On the API page, navigate to the Cases section.
Select POST /crs/api/v2/custom-case-data/files
In the Parameters table, select Add string item, then Choose File to select the Case Metadata file from local storage.
[Optional] To upload multiple files, select Add strong item and Choose File again. Upload up to 5 files. Accepted file types: CSV. Each file should not exceed 10MB in size, with a combined files limit of 50MB.
[Optional] Enter the applicable language in the Description field.
Select Execute.
❗ For more details about Case Metadata files including error messages, downloading, editing, uploading, and tracking upload progress, see Custom Case Data Upload.
Custom Annotations allows you to attribute annotations (labels, scores, and population frequency) to variants or variants within a genomic region. The supported data categories for custom annotation in Connected Insights are as follows:
Filter: String labels
Score: Numeric values
AlleleFrequency: Allele frequency for population frequency data
When matching annotations for large variants (structural variants and copy number variants), by default Annotation Overlap (measured as the total overlap divided by the length of the annotation) of >= 0.75 is used, but can be changed to Reciprocal Overlap (measured as the total overlap divided by either the length of the annotation or the length of the variant, whichever is larger) by specifying Reciprocal Overlap in the Description column for the annotation. For more information, refer to Custom Annotation File Format.
On the top toolbar, select Configuration, and then select the Test Components tab.
Navigate to Custom Annotations and select New.
Download the attached template.
Edit the file with the desired annotations (refer to linked documentation above).
Upload the file.
On the top toolbar, select Configuration, and then select the Test Components tab.
Select the Custom Annotations section.
Select the desired custom annotation.
Select Download.
Connected Insights requires you to provide a report template for each test definition to ensure consistency of reports produced across cases. This section summarizes the actions that can be performed with report templates to customize the look and content of PDF reports to your specifications.
Create several report templates and use them in more than one test definition.
Use a default report template provided by Connected Insights or customize the report as needed. These customizations include: – Changing the logo of the laboratory. – Changing the report name. – Reformatting the page and date. – Removing parts of the report related to the Nothing Reported section. This modification might be needed if the laboratory prefers not to report pertinent negatives. – Adding sample information alongside case and subject information. – Changing text in the Supplemental Information section.
For more information on the customization options, refer to Report Customizations.
On the top toolbar, select Configuration, and then select the Test Components tab.
Navigate to Report Templates and select New.
Select Download the template.
Save the base ODT template.
Edit the file with an applicable document editor. The document editor must be able to load v1.3 ODT files. For information on making custom edits to the report, refer to Report Customizations.
Select Upload template to re-upload the template with the recently made changes. Uploaded files must in the ODT format.
Select Confirm Report Creation when the report preview displays. Download the original report in the ODT format at any time. You can also archive and unarchive report templates. Archiving a report template makes it unavailable for use when creating a test definition.
On the top toolbar, select Configuration, and then select the Test Components tab.
Select Report Templates, and then select Pre-configured Demo Report Template or Pre-configured Demo Report Template (Version 2).
After the report loads, select Download as ODT.
On the top toolbar, select Configuration, and then select the Test Components tab.
Navigate to Report Templates and select New.
For Create your new report, select Upload template.
Using file explorer, navigate to the template with the changes and select Open.
Review the PDF preview to make sure that the modified report displays as intended.
Variant flag groups allow you to organize variants later in the case interpretation. You can add flags for common tasks such as follow-up or to track review statuses.
On the top toolbar, select Configuration.
Select the Test Components tab.
In the left-hand pane, next to the Variant Flag Groups accordion, select New.
In the right-hand pane, enter a Variant Flag Group Name.
Enter a Flag Name.
Choose a flag color.
Select Add.
Create additional flags as needed.
Use the drag handles to change the order that data are displayed in Connected Insights and the final report.
Select Save. The variant flag group appears on the left-hand accordion menu. Select through the flag groups to display previews.
Select Duplicate to duplicate a flag group.
Select Archive to make the flag group unavailable when you create a test definition.
Use an API to ingest cloud analysis data in Illumina Connected Analytics (ICA) into Connected Insights as follows.
From the API page, navigate to the Cloud Analysis section.
Select POST /crs/api/v1/analysis-molecular-data/ica/ingest-ica-analysis.
In the Parameters table, update the description for the following required parameters:
analysisProjectId — The ICA project ID that contains the analysis. To retrieve this ID, open the ICA project containing the analysis and copy the ID from the URL (for example, https://{ICA-host-name}.illumina.com//ica/projects/{analysisProjectId}/projectDetails
).
analysisId — The ICA analysis ID. To retrieve this ID, open the ICA project containing the analysis, open the desired analysis, and copy the ID value from the ID field.
[Optional]Update the description for one of the following optional parameters:
workflowId — The workflow ID for the Connected Insights pipeline that will be used to ingest the analysis data. Note, the associated test definition will be applied. To retrieve this ID, go to the Connected Insights Configuration page, General tab, Data Upload section, and select From Illumina Connected Analytics to view the ICA Pipeline workflows. Select the menu icon within the desired workflow and select Copy Workflow Id.
pipelineId — The ICA pipeline ID used in the desired analysis. To retrieve this ID, open the ICA project containing the analysis, open the desired analysis, find the pipeline listed here and open it, open the pipeline, and copy the ID value from the ID field.
❗ Enter either the specific workflow or pipeline ID.
autoGenerateCaseId — Select either true or false for the system-generated case ID (the default value is false).
tags — Tag names associated with the case that can be used for a full or partial search.
analysisStatus — Enter either SUCCEEDED or FAILED for the analysis status from ICA for the run (the default is SUCCEEDED).
Accept-Language — The applicable language for the data.
Select Execute.
The Variant Filters section describes how to add, configure, duplicate, or archive variant filters.
On the top toolbar, select Configuration.
Select the Test Components tab.
Navigate to Variant Filters and select New.
Navigate to the Condition Group section and enter the applicable genes in the Genes field.
[Optional] Select the Include genes from diseases check box.
Select Apply.
Select Include or Exclude from the drop-down list for each gene.
For Variant Category, select the field to open up a drop-down list of variants that can be included or excluded.
Select the check boxes next to the applicable variant types.
Select Add Criteria and select the applicable criteria from the drop-down list (for example, Cancer Hotspot Samples).
Select Include or Exclude from the drop-down list for the criteria.
To include or exclude additional criteria, repeat steps 10 and 11.
For AND or OR, select Add Condition Group to add any other applicable condition groups.
[Optional] Select Reset to undo the changes to the condition groups.
Select Save.
On the top toolbar, select Configuration.
Select the Test Components tab.
For Variant Filters, select a filter.
Select Edit.
Update the applicable settings. For more information, refer to Add and Configure a Variant Filter.
Select Save.
On the top toolbar, select Configuration.
Select the Test Components tab.
For Variant Filters, select the applicable filter.
In the right-hand pane, select Duplicate.
[Optional] Adjust the condition group settings. For more information, refer to Add and Configure a Variant Filter.
Select Save.
On the top toolbar, select Configuration.
Select the Test Components tab.
For Variant Filters, select the applicable filter.
In the right-hand pane, select Archive.
To confirm, select Yes, change.
Use APIs to perform the following tasks in Connected Insights:
Retrieve, edit, and delete case information including disease and case metadata. For more information, refer to Case APIs.
For Connected Insights - Cloud, ingest cloud analysis data. For more information, refer to Ingest Cloud Analysis Data API (ConnectedInsights - Cloud Only).
Pull report information, including PDF report drafts and case data. For more information, refer to Report APIs.
Before using the APIs, make sure that the following prerequisites are met:
Access to the Swagger site. Access this site by appending /api-docs
to the Connected Insights host URL using one of following URL formats:
For Connected Insights - Cloud, use the URL format https://<domain>.connectedinsights.illumina.com/api-docs
For Connected Insights - Local, use one of the following URL formats depending on whether a fully-qualified domain name is configured:
If fully-qualified domain name is configured, use the URL format https://<DRAGEN server hostname>.<domain name>/api-docs
If fully-qualified domain name is not configured, use the URL format https://<DRAGEN server IP address>/api-docs
For Connected Insights - Local, the URL will follow the same format as the URL used to login to Connected Insights (for example, if the login URL includes an IP address, the API URL will also include an IP address).
Know the following authorization values. Instructions for finding all 3 of these values are below:
Authorization (apiKey or psToken/iasPsToken)
X-ILMN-Domain
X-ILMN-Workgroup
An API key or psToken/iasPsToken may be used. Consider the following before proceeding:
❗ Note the limitations below for API keys for Connected Insights - Cloud only:
Regenerating an API key will break Data Uploaders using it until API key in the uploader config file is updated.
If using the maximum number of API keys, consider using the psToken instead of regenerating an API key or deleting then creating a new API key.
If using a global API key, API actions will be limited to the workgroup used for the X-ILMN-Workgroup authorization.
If using an API key, it is retrieved from the Manage API Keys section of Connected Insights. Retrieve the API key as follows.
From anywhere in Connected Insights, click your username in the top-right, then select Manage API Keys.
Click Generate, enter an API key name, then select workgroups and application roles.
Selecting All current and future workgroups and roles (Global API Key) will still cause API actions to only occur in the workgroup for the X-ILMN-Workgroup authorization you provide later in Swagger. Selecting this option does not mean all API actions will occur in all workgroups.
You may use an existing API Key if you recorded it and it pertains to the desired workgroup(s) and application role(s). For Connected Insights - Cloud users, consider the limitations above before regenerating an existing API Key.
Click Generate and copy the API key.
This is the one time this value can be viewed. If you will use it again in the future, record and store the API key securely and do not share it with others. You cannot recover it later.
In another tab or window, go to the Swagger site. Select Authorize, then in the Available authorizations window, type ApiKey
(including one space after) as a prefix followed by the API key value (for example, ApiKey <API key value>
)
Select Authorize.
If using a psToken, it is retrieved from browser metadata where Connected Insights is being accessed:
In Connected Insights browser window, right-click and select Inspect.
From the Inspect pane, navigate to the top toolbar and select Application.
In the Storage section, select Cookies, then select the menu option with the same name as the Connected Insights URL.
In the Name column, copy one of the following values depending on whether you are using Connected Insights - Cloud or Local:
For Connected Insights - Cloud, select psToken and copy the psToken value that displays at the bottom of the pane.
For Connected Insights - Local, select iasPsToken and copy the iasPsToken value that displays at the bottom of the pane.
In another tab or window, go to the Swagger site. Select Authorize, then in the Available authorizations window, paste the psToken or iasPsToken value in the Authorization (apiKey) section Value field. No prefix is required before the psToken or iasPsToken value.
Select Authorize.
The domain name is retrieved from the URL.
For Connected Insights - Cloud, retrieve the domain name as follows:
Copy the domain name from the URL for Connected Insights. For example, <domain>
from https://<domain>.connectedinsights.illumina.com
. Note that only the domain name is needed, not the entire URL.
In the Swagger Available authorizations window, enter the domain name into the X-ILMN-Domain (apiKey) section Value field.
Select Authorize.
For Connected Insights - Local, retrieve the domain name as follows:
From the Connected Insights URL, the following information from one of the Connected Insights URLs depending on whether a fully-qualified domain name is cofigured or not:
Copy the DRAGEN server v4 hostname if fully qualified Domain Name is configured. For example, <DRAGEN server v4 hostanme>
from https://<DRAGEN server v4 hostname>.<domain name>/
. Note that only the hostname is needed, not the entire URL
Copy the IP address of the DRAGEN server v4 if the fully-qualified Domain name is not configured. For example, <DRAGEN server v4 IP address>
from https://<DRAGEN server v4 IP address>/
.
In the Swagger Available authorizations window, paste the copied hostname or IP into the X-ILMN-Domain (apiKey) section Value field.
Select Authorize.
The workgroup ID is found in the metadata of the Connected Insights browser. Retrieve the workgroup ID as follows.
In Connected Insights, right-click and select Inspect
On the Inspect pane at the right of the screen, navigate to the top ribbon and select Application. A pane opens to the left of the Inspect pane.
Navigate to the Storage section and select Cookies.
From the Name column, select olympia-current-workgroup and copy the Cookie Value that displays at the bottom of the pane (for example, a1bc2efg-h3i4-567j-8901-k23l45mno6p7
).
In the Swagger Available authorizations window, paste the copied workgroup ID into the X-ILMN-Workgroup (apiKey) section Value field.
Select Authorize.
Use APIs to pull reports (signed-off and draft) and case data, including the subject, sample, and report details. The reports are in a PDF output, and case data is in a JSON output.
Use this API to pull a PDF of the report for a case. If the report is a draft (e.g., case status is not "Report(s) Signed-Off"), the PDF will include a watermark stating "DRAFT".
From the API page, navigate to the DrsPullController section.
Select GET /drs/{apiVersion}/draftreport/case/{caseId}/reports/{reportId}/pdf
In the Parameters table, update the description for the following required parameters:
apiVersion — This value should be v1
.
caseId — The case ID for the case. To get this information, open the case in Connected Insights and copy the case ID from the URL (for example, https://{domain}.connectedinsights.illumina.com/interpretation/{caseId}/reports/{reportId}/draft-report
).
reportId — The ID associated with the report. To get this information, open the case in Connected Insights, go to the Report page, and copy the report ID from the URL (for example, https://{domain}.connectedinsights.illumina.com/interpretation/{caseId}/reports/{reportId}/draft-report
).
[Optional]Update the description for the following optional parameters:
Accept-Language — The applicable language for the data.
reportLanguage — The applicable language for the generated report.
Select Execute.
Use this API to pull case data in JSON format. Case data includes subject, sample, and report details. If the report is a draft (e.g., case status is not "Report(s) Signed-Off"), the JSON will include the information in the draft report.
From the API page, navigate to the DrsPullController section.
Select GET /drs/{apiVersion}/draftreport/case/{caseId}/reportjson.
In the Parameters table, update the description for the following required parameters:
apiVersion — This value should be v1
.
caseId — The case ID for the case. To get this information, open the case in Connected Insights and copy the case ID from the URL (for example, https://{domain}.connectedinsights.illumina.com/interpretation/{caseId}/reports/{reportId}/draft-report
).
[Optional] Update the description for Accept-Language with the applicable language for the data.
Accept-Language — The applicable language for the data.
Select Execute.
This section describes how to upload data with Connected Insights and includes setup instructions. Connected Insights requires the following data types:
Secondary analysis output data — Connected Insights is compatible with a broad range of analysis pipeline outputs. To configure the input file format, select a compatible pipeline (for example, DRAGEN TruSight Oncology 500 v2.5.2) or configure a custom pipeline.
Case, subject, and sample data — For more information on custom case data, refer to Custom Case Data Upload
Connected Insights - Cloud allows data upload from the following sources:
User storage — Data ingestion is managed by the Data Uploader tool that supports uploading variant call format (VCF) files and other analysis output files. For more information, refer to Data Upload from User Storage (Connected Insights - Local Storage).
Cloud storage on ICA — Data ingestion can be configured through the Data Upload page or API. For more information on using the Data Upload tab or API, refer to Data Upload from ICA (Connected Insights - Cloud).
Before uploading, create the following items:
Custom case data (if applicable)
Test components
Test definitions For more information on creating test components and definitions, refer to Test Definition Setup.
Connected Insights - Cloud includes an Illumina Connected Analytics pipeline that supports data uploads from ICA to defined workflows.
You must be a member of the workgroup to which the data is uploaded. A project not linked to the workgroup must be given permissions at the level of Contributor in the Team tab of ICA to be accessible from Connected Insights. User must have "Lab Director" role for Connected Insights to run the ici-uploader. For more information on adding users to a workgroup and adding permissions, refer to ICA team management.
This section provides instructions for adding a supported ICA pipeline.
In Connected Insights, select the gear in the top-right corner to open the Configuration page.
Select the General tab.
Select Data Upload.
Select the From Illumina Connected Analytics tab.
For Cloud Pipelines, select Add.
For Choose compatible pipeline from the catalog, select the applicable pipeline from the drop-down list, refer to Supported Pipelines.
For Test Definition, select the applicable definition.
Select Save.
ℹ️ For the configured Illumina Connected Analytics Pipeline, Connected Insights will automatically upload new analyses in ICA for the specified workflow. When data is uploaded, the status to the right of the workflow name will show the last analysis upload date. If a new project is created or linked after the configuration is made, it will need to be refreshed by editing and saving the configuration before it will begin to pick-up data from that project.
Locate the pipeline, and then select ...
Select Delete.
When prompted, select Yes, Remove.
This section provides instructions for manually uploading a completed analysis for a supported ICA pipeline.
From the Case List, select + New Case.
Select the Import from Connected Analytics option and click the button for Import from Connected Analytics.
Ensure the correct project is selected under Select Project.
Select the desired analysis to upload and click the button to Continue.
[Optional] Select a case metadata file to upload (up to five files may be uploaded at one time), refer to Custom Case Data Upload
Click Review.
Review the information and click Submit to begin processing the selected analysis.
❗ The user must first configure the pipeline in Data Upload Configuration, see above, before manually uploading analyses from ICA.
Use an API to upload data to Connected Insights - Cloud. For more information, refer to Ingest Cloud Analysis Data API (Connected Insights - Cloud Only).
Connected Insights accepts metadata information about case, subject, and the sample in CSV format to use it for the case creation, display, and reporting.
Overview of uploading custom case data. Each step is further detailed below:
Download the Case Metadata template file from the Connected Insights Cases page.
Edit the Case Metadata template file to include the desired data.
Upload the Case Metadata file via the Connected Insights user-interface, Data Uploader, or API.
Download the Case Metadata template file from Connected Insights:
Navigate to the Connected Insights Cases page.
Select Upload Case Metadata (top-right corner of the page).
Select Upload CSV.
Click attached template to download the Case Metadata template CSV file.
❗ Starting from the template can help guide formatting, however, any CSV file that follows the content formatting requirements detailed below can be used to upload case metadata. Files containing non-English characters must be encoded as UTF-8.
Edit the case metadata file to add and correctly format the desired information. See the example at the bottom of this subsection:
Open the CSV file with software capable of editing CSV files (for example, a text editor; if using Excel, be cautious of potential unexpected formatting and character additions).
Ensure the following formatting requirements are met:
The first row must contain the headers of the fields to be updated. Each subsequent row contains data.
Each row must contain information in the Sample_ID
and Case_ID
columns. Sample_ID
values are case-sensitive.
Fields that require a date must be in yyyy-mm-dd format.
Tumor_Type
values must be the SNOMEDCT ID for the disease.
The SNOMEDCT ID can be found by navigating to an existing case and searching for the disease in the Case Details or assertion form. It can also be found by navigating to the Configuration page, Disease Configuration section, clicking New +, then searching in Associated Disease Term(s). Lastly, the ID can also be found by using the International Edition browser at the SNOMED International SNOMED CT Browser website.
When the tumor type is unknown, SNOMETCT ID 363346000
("Malignant neoplastic disease") or 255052006
("Malignant tumor of unknown origin") can be used. However, the accuracy of actionability will be higher the more specific the tumor type provided is.
All other columns must follow formatting requirements specified in the Case Metadata template file.
Data in columns for fields defined in the Custom Case Data Definition section of the Configuration page must match the formatting requirements based on whether the data type is text, a number, or a date (for details, refer to Custom Case Data Definition).
Once all rows are added, save.
Refer to the following formatting example:
Case metadata can be uploaded in three ways. See below for instructions on each method:
Upload from local storage via Connected Insights user-interface.
Upload from local storage via the Data Uploader.
Upload from local storage via an API.
Upload Case Metadata files via the Connected Insights user-interface
Navigate to the Connected Insights Cases page.
Select Upload Case Metadata (top-right corner of the page).
Select Upload CSV.
Upload the file.
Upload Case Metadata files via the Data Uploader
Install the Data Uploader in a location with access to the Case Metadata file (refer to Data Upload from User Storage). Proceed to the next step if it is already installed.
Ensure the Case Metadata file is in a location accessible by the Data Uploader.
Create a new pipeline or edit an existing pipeline and set the Choose a folder to monitor for case metadata (optional) field to the file path of the directory containing the Case Metadata file (refer to Data Upload from User Storage).
Next time the Data Uploader daemon runs, the file will be ingested (may be ~10-15 minutes).
Upload Case Metadata files via an API
Refer to Case APIs, subsection "Upload Metadata files via an API".
Update case metadata of an existing case
To update an existing case, use the Sample_ID
and Case_ID
of the existing case and add updated information in additional fields. It may be useful to use an API in the Case Metadata section of the API page to retrieve the existing case metadata for a case (for details on using APIs, see APIs). The overwriting and preservation logic is as follows:
Overwriting Logic: If data conflicts, new data will overwrite existing data. For the Tags
field, new data will be added as an additional tag and will not overwrite any existing tag(s).
Preservation Logic: Existing data will not be overwritten if the data for the field is the same as existing or no data is entered. Additionally, fields not included in the Case Metadata file will not be affected (for example, if the Case Metadata file does not include the Date of Birth
field, existing data in that field will not be updated).
Create a new case by uploading a Case Metadata file
To create a new case, use a new Sample_ID
and a new Case_ID
and upload the Case Metadata file before ingestion of molecular data (for example, VCF files or other secondary analysis output files).
In order for the molecular data to associate with the correct case metadata, the Sample_ID
and Case_ID
must match (for example, the Sample_ID
value used in the Case Metadata file should match the Sample_ID
value in the sample sheet).
Cases created this way will have a Status column value of Awaiting Molecular Data and a Workflow Name column value of N/A in the Case List on the Cases page. The Status and Workflow Name will update after completely uploading molecular data.
The Case Metadata Uploads page displays Case Metadata file upload history and error messages:
Navigate to the Connected Insights Cases page.
Select Upload Case Metadata (top-right corner of the page).
Select View Past Uploads.
The table displays Case Metadata file upload history, status, and details.
If errors occur, the Details column will state this and provide a link to download a copy of the Case Metadata file annotated with error messages for each row.
Use this API to get the Audit Log information in Connected Insights. Search audit logs for cases, subjects, samples, analysis, etc.
On the API page, navigate to the AuditLog section.
Select GET /als/api/v1/auditlogs/search.
In the Parameters table, update the description for the following applicable parameters:
caseId — The displayed case ID (for example, ILM-ABC-234) or the ID for the case (for example, https://{domain}.connectedinsights.illumina.com/interpretation/{caseId}/reports/{reportId}/overview
).
userDisplayId — The email of a user's Connected Insights account (for example, esong@company.com).
entityId — The ID of a specific Case, Sample, Subject, or Analysis.
entityType — A type of entity. An entity is something within Connected Insights (e.g., user
or subject
). Refer to the the complete list of Entity Types below.
eventName — A type of event that occurred in Connected Insights (e.g., case.added
or molecular-data.deleted
). Refer to the the complete list of Event Names below.
toDate — Include audit log entries created on and before this date. This date is in the yyyy-MM-dd'T'HH:mm:ss'Z' format (for example, 2021-01-30T08:30:00Z).
fromDate — Include audit log entries created on and after this date. This date is in the yyyy-MM-dd'T'HH:mm:ss'Z' format (for example, 2021-01-30T08:30:00Z).
pageNumber — The specific page number of the API response.
pageSize — The size of each page in the API response.
Select Execute.
actionability-classifications
assertion
biomarker
case
cli-log
custom-annotation
custom-case-data
data-upload
disease-configuration
domain
filter
flag-groups
ici-uploader
molecular-data
pipeline-configuration
preferred-transcript
qc-configuration
report
report-automation
report-category
report-footer
report-summary
report-template
sample
subject
case.added
case.analysis.linked
case.assertion.updated
case.biomarker.status.updated
case.deleted
case.disease.added
case.disease.updated
case.metadata.added
case.metadata.updated
case.molecular-data.added
case.report.added
case.report.deleted
case.report.json.viewed
case.report.pdf.viewed
case.report.status.reset
case.sample.added
case.status.updated
case.subject.added
case.subject.updated
case.tags.updated
case.updated
case.viewed
domain.project.added
file.metadata.added
file.metadata.error
file.metadata.processed
file.metadata.processing
ici.uploader.downloaded
molecular-data.added
molecular-data.cloud.ingestion.added
molecular-data.deleted
molecular-data.updated
sample.metadata.added
sample.metadata.updated
subject.deleted
subject.metadata.added
subject.metadata.updated
subject.renamed
subject.transferred
Connected Insights - Cloud Data Uploader tool supports uploading of VCF files and analysis output for user-provided machines and storage devices and can be downloaded from Configuration -> Data Upload section of the application.
Connected Insights - Local Connected Insights - Local includes the Data Uploader tool that is installed on the DRAGEN server v4 as part of the Connected Insights - Local installation and reads secondary analysis results from the external storage drive that is configured. The Data Uploader tool is detected and identified as Default-CLI-Installation in the Data Upload section of the Configuration page. If Default-CLI-Installation does not show as Online, refer to Software Errors and Corrective Actions.
The Data Uploader logs can be found at /staging/ici/logs/tss-cli/
. With Connected Insights - Local, these logs can also be downloaded from the Activity tab in the Case Details pane on the Cases page. For more information, refer to Case Details.
The secondary analysis input logs can be found /ExternalStorageDriveMountPath>/d53e4b2d-0428-4b3e-92bf-955f7153c360/d53e4b2d-0428-4b3e-92bf-955f7153c360/upload-logs/<DataUploadConfiguredMonitoringLocation>/<SecondaryAnalysisRunFolder>/run_<Timestamp>.json
This section identifies the requirements for uploading data from user storage, enabling ingestion from the network drive, and adding an existing pipeline. For Connected Insights - Cloud, this section also covers how to download and install the Data Uploader tool and has instructions for generating an API key.
To upload data from user storage, the following requirements must be met:
Make sure you have Java 8 or a newer version installed on your computer. You can check by opening a terminal or command prompt and typing java -version. If you don't have it installed, you can download and install it from the official Java website.
Data Uploader with Java Virtual Machine (JVM) 8+ that is compatible with Mac, Windows, or Linux CentOS.
An API key and access to the workgroup to which the data is uploaded. The API key comes with the installer. To generate a newAPI key, refer to [Optional] Generate an API Key.
Administrator access on the computer where Data Uploader is installed.
Before you begin, perform the following actions:
Create custom case data.
Create test components.
Create test definitions.
For more information, refer to Configuration.
Download and install the Data Uploader tool as follows.
In Connected Insights, select the gear at the top right of the page.
In the General tab, under Data Upload, select the From Local Storage tab.
Under Download and Launch the Data Uploader, select the storage device operating system from the drop-down list.
Select Download Data Uploader. A progress bar displays during the download.
Copy the installation directory of the storage device. Make sure that Data Uploader is in a location that has access to your secondary analysis output folder.
Use the following tar command to extract the files: Replace {ici uploader script}
with the applicable file name. tar xvzf {ici uploader script}.tar.gz
❗ Extracting files can vary depending on the operating system. Most terminals support the tar command. For Windows, you can use a zip file extraction application (eg, 7-Zip) to extract the content of the tar folder.
Make sure that the files in the following table are in the unzipped Data Uploader file.
Install Data Uploader as follows:
a. [Windows] Start the command prompt as an administrator and run ici-uploader.exe install
.
❗ For windows environment, user must be in the installation directory to install/uninstall the application.
ici-uploader.exe start-daemon
b. [Mac and Linux] Run the following command on the terminal ./ici-uploader install
❗ If the installation fails, start the Connected Insights installation manually using
ici-uploader start-daemon
c. Follow any prompts in Data Uploader. d. Enter your API key and press Enter.
❗ If you did not download with an auto-generated API key, provide one to the installer when prompted. If you are installing Data Uploader for the first time, you must generate an API key. For more information, refer to [Optional] Generate an API Key.
e. Under Define and Monitor Data Uploads, make sure that your machine displays.
Data Uploader is now set up for auto and manual ingestion. You can also change the name of the installed Data Uploader by selecting ... and Edit Server Name . If you must download any logs associated with the Data Uploader from the last 24 hours, select ... and Download Logs.
❗ If the user is not a system administrator, the daemon can be started with the
ici-uploader start-daemon
command for Mac/Linux or with theici-uploader.exe start-daemon
command for Windows. This command does not run the process as a system service and requires you to start and stop the service manually. To stop the daemon, run the commandici-uploader stop-daemon
After Data Uploader has been downloaded and installed on the user storage, you can set up configurations for the tool to upload data into Connected Insights automatically. Each configured pipeline monitors user storage for new molecular data.
f. User can stop the ici-uploader (running as system service) using the following command ici-uploader stop-service
command for Mac/Linux or with the ici-uploader.exe stop-service
command for Windows. User can start the uploader via ici-uploader start-service
.
❗If data-uploader is already running as system-service, and user also runs the uploader manually via
ici-uploader start-daemon
, it may cause issues. User must stop already running data-uploader withici-uploader stop-service
before starting uploader manually.
If you are using Linux, automatic case upload is already enabled and this section is not applicable. For Mac, contact Illumina Technical Support. For Windows, run the "illumina ICI Auto Launch Service" to make the network drive available for Data Uploader as follows:
When the Data Uploader is running, open the Services application from the Start menu and locate the "illumina ICI Auto Launch Service".
Right-click "illumina ICI Auto Launch Service" and select Properties from the drop-down menu.
In Properties, select the Log On tab and enter your account ID and password. Confirm the password.
Select the General tab.
Select Stop, then select Start to start the service. The network drive is available for ingestion for Data Uploader.
After completing these steps, the Data Uploader details are visible in Connected Insights.
If the computer where the Data uploader is installed is behind a proxy server, then Uploader proxy setting must be enabled. Before you install the Data Uploader, run the following command on the terminal (Linux).
❗ export JDK_JAVA_OPTIONS='-Dhttps.proxyHost=<IP address of the proxy server e.g. 1.2.3.4> -Dhttps.proxyPort=<Port of the proxy server e.g. 8080>'
For Windows, it can be set via following command.
❗ setx JDK_JAVA_OPTIONS "-Dhttps.proxyHost=<IP Address of the proxy server e.g. 1.2.3.4> -Dhttps.proxyPort=<Port of the proxy server e.g. 8080>"
Remember to replace and with the actual values you need.
In Configuration Settings, select the radio button next to Choose compatible pipeline from catalog, refer to Supported Pipelines.
Select a pipeline from the drop-down list (for example, DRAGEN TruSight Oncology 500 Analysis Software v2.5.2).
❗ When running the DRAGEN Somatic Whole Genome pipeline in the Tumor-Only mode, you must set
--output-file-prefix
to matchsample-id
(the RGSM of the sample in the FASTQ list) of the run.
For Test Definition, select the applicable definition.
For Choose a folder to monitor for case metadata (optional), enter the path for the folder in the secondary analysis folder created by Data Uploader.
Select Save.
If you are using Data Uploader for the first time, then you must generate a new API key. All Data Uploader operations require an API key for authentication. The Data Uploader bundle can be downloaded with an autogenerated API key. If the bundle includes an API key, skip this section.
❗ If you are installing Data Uploader on multiple machines, manually create and track your API key by running the following auto-updating and manual run command:
ici-uploader configure --api-key={apiKey}
Make sure that the API key is within single quotation marks (for example,'{SYSTEM_API-KEY}'
)
In Connected Insights, select Manage API Keys from the Account drop-down menu.
Select Generate.
Enter a name for the API key.
To generate a global API key, select All workgroups and roles.
Select Generate.
In the API Key Generated window, select one of the following options:
Show — Reveals the API key.
Download API Key — Downloads the API key in .TXT file format.
Select Close after you have stored the API key.
❗ The API key cannot be viewed again after closing this window. Download the API key or save it in a secure location.
The API key is added to the Manage API keys list.
Perform any of the following actions in the Manage API Keys list:
Select Regenerate to generate a new API with the existing API key name.
Select Edit to edit the API key name or change the workgroups and roles selection.
Select Delete to delete the API key.
The following information is applicable to both Connected Insights - Local and Connected Insights - Cloud. Create each configuration as follows.
Input the {monitoring location} for secondary analysis output.
The monitoring location is the full path to the location where secondary analysis output data is deposited in user's storage.
For example:
/rest/of/storage path/{monitoring location}/{runFolder}/{sample folders, sample sheet, inputs, tumor_fastq_list.csv}
For DRAGEN server v4 standalone results:
/rest/of/storage path/{monitoring location}/{sample name folders}/{sample sheet, inputs, VCFs, .bams}
Associate the workflow schema for this pipeline. a. Under Choose compatible pipeline from the catalog, select the applicable pipeline from the drop-down list (for example, DRAGEN WGS Somatic v4.2). b. If you are running a custom workflow, then upload a workflow schema that corresponds to the data that the configuration uploads. For more information, refer to Custom Pipeline Configuration.
Select the test definition to be associated with cases created by this configuration. For more information, refer to Test Definition Setup.
[Optional] Input the location where custom case data is stored. This location is the full path to where custom case data is deposited in user storage. For more information, refer to Custom Case Data Upload.
Select Save to complete the configuration. If Data Uploader is running, it monitors this configuration for data upload.
Perform any of the following actions below:
Edit You can modify the pipeline configuration by clicking "Edit" against a configuration.
Note: The change in configuration does not impact the Case that are already ingested.
Delete You can delete the pipeline configuration by clicking "Delete" against a configuration.
Requeue (Connected Insights - Local) You can resume or reupload a secondary analysis output folder by clicking "Requeque" against a configuration. Upon clicking "Requeue", application will re-attempt to create the case from the run folders which previoulsy failed due to one of the below errors:
SampleSheet validation error
Case ingestion has stopped due to zero GEs balance
Case ingestion has stopped due to low space on external mounted storage or /staging
Upload an analysis output by running the following command:
ici-uploader analysis upload --folder={path-to-analysis} --pipeline-name={pipelineName}
--folder {path-to-analysis}
— The absolute path to the analysis output to upload into Connected Insights. This folder contains the sample sheet.
--pipeline-name={pipelinename}
— The name of the pipeline created in Connected Insights to apply to cases uploaded from this analysis. Pipeline names must include only letters, numbers, underscores, and dashes. The name cannot include spaces or special characters.
[Optional] --runId={path-to-config}
— The id of the run to be created in place of the run ID determined by the run folder name.
[Optional] --pair-id={pair-id}
— The pair-id of the analysis to upload from the Sample Sheet when limiting upload to a single analysis.
[Optional] --case-display-id={case-display-id}
— The id of the case to be created in place of the pair-id when uploading a single analysis with --pair-id={pair-id}
.
[Optional] ici-uploader logs show
— Run to display the logs in ICI_Data_Upload_log.json.
[Optional] Downloads > ici-uploader logs download
— Download Data Uploader logs in a zipped folder by running the command prompt.
Upload the custom case data file associated to one or more cases by running the following command:
ici-uploader case-data --filePath={absolute-path-of-csv-file}
For more information on custom case data files, refer to Custom Case Data Upload.
The following table shows the approximate time it takes for example datasets to upload and receive the Ready for Interpretation status. The duration is evaluated by analyzing a batch of samples ingested through the Connected Insights tertiary analysis in conjunction with the DRAGEN secondary analysis performed on similar datasets on the DRAGEN server v4.
Connected Insights directly supports the following pipelines:
Previous interpretations can be uploaded to My Knowledge Base at any time (for example, during onboarding) so you can immediately start prioritizing variants and reporting based on information from your lab.
Navigate to the app selector (grid icon) at the top-right of the screen and select My Knowledge Base.
In My Knowledge Base, under Add New Knowledge, select Add Assertions.
Select attached template to download the upload template.
Edit the template by adding values to the columns. For more information on the applicable columns and values, refer to and . To view existing assertions as examples, refer to .
After editing, save the file in the CSV format. The maximum permitted file size is 10 MB.
Upload the template file. For more information, refer to .
The template is in CSV format and contains the following columns:
If using Excel, make sure that no auto-formatting has occurred.
After the content has been added to the template, it can be uploaded for processing.
In the Add Assertions dialog, drag and drop or select the file to upload. The maximum permitted file size is 10 MB. Any initial validation errors are displayed (for example, missing required headers, incorrect file type).
After the file has been uploaded, view the processing status for each file by selecting View Uploads.
When completed, view the number of rows processed, including rows that have issues. If a file has issues, download the file and view the issues in a new error column provided in the download. Issues can be resolved in the file and re-uploaded.
Upload gene descriptions through the CSV template used to upload assertions. To upload gene descriptions, the following fields are required:
type (for the gene description, the value must be Gene Information)
geneRoles
summary
biomarkerType
level (for the gene description, the value must be Gene)
genomeBuild
geneSymbol
nbciGeneId
Assertions in the knowledge base, created either by upload or within a case, can be downloaded at any time.
In the My Knowledge Base screen, select Download to View.
Connected Insights imports variant calls for the following variant types in the Variant Call File (VCF) file format (v4.1 and later):
Small variants (SNVs, MNVs, and small indels)
Structural variants (SVs)
Copy number variants (CNVs)
RNA fusion variants
RNA splice variants
❗ Imported VCF files must contain at least one sample and be sorted correctly to ensure valid display of results in Connected Insights.
The following sample fields are supported for each variant type:
¹ The following GT values are interpreted as an absence of the reported variant and are not imported:
.
./.
0
0/0
¹ The following GT values are expected given the CN of the variant:
0
: The copy number is normal in a region expected to be haploid.
1
: The copy number differs from normal in a region expected to be haploid.
0/0
: The copy number is normal in a region expected to be diploid.
0/1
: The copy number differs from normal and is not a complete loss in a region expected to be diploid.
1/1
: The copy number is a complete loss in a region expected to be diploid.
¹ The following GT values are interpreted as an absence of the reported variant and are not imported:
.
./.
0
0/0
After uploading secondary analysis results, use Connected Insights to set up filtering, modify table views, and manage the case through the Cases page.
The Cases page provides a quick view of the following information:
Cases
Case statuses
Usage data
This page is used to track the status of cases through your lab, find cases that need attention, or start new cases.
The Cases page displays the number of cases for each case status and sub status.
Select a status to open the Cases page with filtered results based on the status.
Select the Cases tab to open the Cases page with all cases listed.
Select View Storage to open the Usage page in the Illumina Analytics Platform.
Add tags to cases and edit disease information in Connected Insights. For more information, refer to .
For Connected Insights - Local, the Cases page also displays the following notifications:
If your Genome Equivalent Sample balance is low, a notification to contact your administrator or Illumina Technical Support displays.
If the storage space in the /staging/
or external mounted directory is below the required space threshold for case ingestion, a notification displays and ingestion stops after reaching capacity. To continue ingestion, free up space.
If the external drive is not accessible, a notification displays and ingestion or case processing will fail. To continue, ensure the external storage drive is accessible.
Do not delete or alter content at the following locations to free up space:
/staging/ici
/<mountedDrive>/d53e4b2d-0428-4b3e-92bf-955f7153c360
/<mountedDrive>/ici_<ServerHostname>/
These locations contain Connected Insights -generated files. If these files are deleted, new cases cannot be processed or case results may not be available.
Component
Description
ici-uploader-daemon.jar
Used to run Data Uploader as a daemon.
ici-uploader.jar
Used to run Data Uploader on demand.
uploader-config.json
This file contains the configuration for Data Uploader to allow it to connect to Connected Insights.
ici-uploader.exe
The installer for ici-uploader on Mac or Windows.
Mac: com.illumina.isi.daemon.plist
The installer for ici-uploader on Mac or Windows.
Linux: com.illumina.isi.daemon.service
The installer for ici-uploader on Mac or Windows.
ici-uploader or ici-uploader.exe
The installer for ici-uploader on Mac or Windows.
wrapper.exe
This file is used to set up Data Uploader as a system service on Windows.
README.txt
Third-party licensing information for Data Uploader.
Sample Size
Duration
CPU Usage
Memory Usage
Network I/O
8 Samples TSO 500 DNA cases with an average of 90,000 variants
55 minutes
88.4%
26.04%
write: 22573.098 kb/s, read: 25442.099 kb/s
8 Samples TSO 500 ctDNA
1h 5m
96.65%
51.0%
write: 288181.985 kb/s, read: 176519.153 kb/s
8 Samples WGS Tumor Normal
15m per sample
97.05%
46.32%
write: 22336.569 kb/s, read: 35373.43 kb/s
8 Samples WGS Tumor Only
3h 41m 21s per sample
94.05%
49.9.32%
write: 377878.867.569 kb/s, read: 197353.179.43 kb/s
Pipeline Name and YAML
Support (Local Storage / ICA)
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage and ICA
Local Storage
Local Storage
Sample Field | VCF Fields | Details |
Allele Depths | AD | The read support for variants called at this position. Expected as a comma separated list of values for the reference allele followed by each alternate allele. |
Total Depth | DP | The total read support for all alleles at this position. Will be calculated as the sum of all allele depths if not provided. |
Variant Read Frequency / Variant Allele Frequency | VF (or derived from AD) | The proportion of reads supporting each alternate allele. Expected as a comma separated list of values for each alternate allele. Will be calculated based on allele depths and total depth if not provided. |
Genotype | GT¹ | The genotype of the sample at the given position. |
Sample Field | VCF Fields | Details |
Fold Change | FC, SM | Estimated fold change for the copy number variant. |
Copy Number | CN | Estimated absolute copy number for the copy number variant. |
Minor-haplotype Copy Number | MCN | Estimated absolute copy number for the minor-haplotype of a copy number variant. When MCN is zero the copy number variant can be determined to be LOH. |
Genotype | (Derived from CN when available)¹ | The genotype of the sample at the given position. |
Sample Field | VCF Fields | Details |
Paired Reads | PR | The paired read support for variants called at this position. Expected as a comma separated list of values for the reference allele followed by each alternate allele. |
Split Reads | SR | The split read support for variants called at this position. Expected as a comma separated list of values for the reference allele followed by each alternate allele. |
Supporting Reads | (Derived from PR and SR) | The cumulative read support from split reads and paired reads for variants called at this position. |
Total Depth | (Derived from PR and SR) | The total reads for all alleles called at this position. |
Variant Read Frequency / Variant Allele Frequency | (Derived from PR and SR) | The proportion of reads supporting each alternate allele. Calculated based on supporting reads and total depth. |
Genotype | GT¹ (or derived from PR and SR) | The genotype of the sample at the given position. |
The Case Details pane contains the following tabs:
Summary
Related Cases
Activity (Connected Insights - Local only)
Select a case, and then select Case Details to open the Case Details pane.
The Summary tab contains the following information:
Case ID — Indicates the unique ID for the case.
Workflow — Indicates the type of analysis available for the case. The workflow name is defined at the user level.
Genome — Indicates the genome build for the case.
Workflow Type — Indicates the type of analysis for this case: DNA, RNA, or DNA + RNA.
Sex — The biological sex of the sample subject: male, female, or unknown.
Disease — The disease associated with the case. Connected Insights allows you to edit this detail. When you change the disease, the case is reprocessed. Any assertions that were made before changing the disease are removed from the report.
Test Definition — The set of default parameters applied to a case when ingested into the platform.
Tags — Helps with organization cases based on free text terms that can be used with the Search function.
Participants — Users in the workgroup that are assigned to the case.
Use the Related Cases tab to do the following actions:
Edit and open cases in the Case Timeline
For Connected Insights - Local, download log files
Change the case subject
Merge cases For more information on merging cases, refer to Merge Cases.
Change the Case Subject
In the Case Details pane, select the Related Cases tab.
Select the pencil icon next to Subject.
In the Subject field, type a subject ID (for example, A).
To confirm the subject change, select Confirm.
In the Case Details pane, select the Activity tab.
Select Download Log Files for this Case.
The ZIP file that is downloaded includes the system technical application log files, data upload logs and case analysis logs. If there is an issue with Connected Insights or you cannot upload case data, these files can be sent to Illumina Technical Support for troubleshooting.
In the Case Details pane, select Edit Case. All available fields accessible for editing are displayed.
Edit or add information about each subject detail.
[Optional] Edit the Disease case detail as follows. a. Under Subject, navigate to the Disease field. b. Enter a disease name. When the tumor type is unknown, "Malignant neoplastic disease (SNOMEDCT: 363346000)" or "Malignant tumor of unknown origin (SNOMEDCT: 255052006)" can be used. However, the accuracy of actionability will be higher the more specific the tumor type provided is. c. When prompted to confirm that you want to change the disease, select Yes, Continue Saving.
[Optional] Add tags to a case or remove them as follows. a. Under Case, navigate to the Tags field. b. Type a tag name and press Enter. c. To remove a tag from a case, select the X next to the tag name. d. To search for or add tags from the Cases page, select the + under the Tags column and enter the tag name. Remove the tag by selecting the X next to the name.
After editing the case details, select Save.
Any restricted custom case data fields are hidden in the case details. These fields are replaced with asterisks. When editing custom case data, the fields are displayed for editing and only a user with lab director permissions can edit, show, or hide these fields. When viewing the draft report, restricted fields are hidden for restricted users and displayed for privileged users.
Reanalyze case action allows you to reanalzye a case that has previously failed. Processing failure could be due to any of the following error conditions:
External storage drive is not accessible or permission have been altered.
Required space is not available on external storage or in /staging
(on the DRAGEN server v4) to process a case.
External storage drive read or write issue due to low or interrupted network bandwidth.
For the reanalysis to succeed, all the required molecular data must be available. To reanalyze a case that failed with a "Has Issues" status, follow below:
Open the case from the Cases page.
Click Case Details in the top-right.
In the Case Details pane, select Reanalyze Case.
Confirm within the pop up.
The case will be submitted for processing with the available molecular data and existing configuration.
The Cases list shows Case IDs for the cases in your workgroup. Connected Insights creates a case for each imported secondary analysis result, and then populates the case with the variants called for the sample. Subject and sample custom case data for each case are entered as part of the custom case data files from the metadata.csv
file which can be picked up through the data uploader (see Data Upload), via an API (see Case APIs), or through the UI (see Case Metadata Upload). From here, you can import analysis results and begin working with a case.
The case status tag provides additional information about the progress of a case from creation to report generation.
Case ID — Indicates the unique ID for the case. Select a case to open it.
Created Date — Indicates the date that the case was created. The default sort is descending.
Status — Indicates the status of the case. – Awaiting Molecular Data — Analysis files not added. – Missing Required Data — The case is missing fields like disease or the required test definition. – Ready for Processing — The case has all required information and is ready for ingestion. – Processing — Annotation and ingestion of the case is in process. – Has Issue — The upload case failed. Select the case for details. Contact Illumina Technical Support for guidance. – Ready for Interpretation — Variants are ingested and ready to be interpreted. – Report(s) Signed Off — Report is approved and signed off.
Workflow Type — Indicates the type of analysis available for this case: DNA, RNA, or DNA+RNA.
[Optional] Sex — The biological sex of the subject: male, female, or unknown.
Disease — The disease associated to the case. It is a required field for processing the case. You can provide disease information from a SampleSheet.csv
, a custom case data file, or add it via the user interface.
Tags — Free text labels associated to the case. You can create new labels by entering a value or use autocomplete to select existing values.
Participants — The users assigned to the case. You can add users from a dropdown of all users that are a member of the workgroup.
❗ If the case data definition is configured, the case and subject level fields display as columns by default.
To delete a case from the Case List grid as follows:
Navigate to the case to be deleted.
Right of the Case Id, select the "..." menu. This menu is only visible to the Lab Director role with the required Illumina Connected Analytics (ICA) permissions. See note below.
Select Delete Case.
Confirm the delete.
❗ The case and any associated subject or sample data, if the subject or sample is not associated to any other cases, is deleted (ICA files, case data, audit log data, variant data, and report data). Case deletion is restricted by role. The user must have the Connected Insights role of Lab Director and the user or the workgroup must have an "ADMINISTRATOR" role in the ICA project associated with the Connected Insights workgroup. The generic format for the ICA Project associated with Connected Insights Workgroup is
ICI_[region]_[workgroup_name]_Project
.
Show, hide, and reorder columns in the Case List grid for a custom view of data in the tab as follows:
Hover over a column header and select the menu button.
To move a column, drag the column to a position in the grid.
Select the menu button next to the column name and change any of the following options:
Pin a column to a position or to the left or right sections of the grid.
Automatically resize the column to display all of the content in the selected column.
Auto-size all columns to display all content for all displayed columns.
Select the filter icon and the sort drop-down menu to filter by keywords and information.
Select the display icon to check or uncheck columns that appear in the Cases list.
The Report tab shows the PDF view of the report generated based on the case information and uploaded data. For more information on how to edit and preview reports, refer to Reports. For more information on how to customize reports, refer to Report Customizations.
Connected Insights includes an embedded Integrative Genomics Viewer (IGV) that can be used to view sequencing reads and evaluate variant quality.
To display the variant in IGV, select the IGV button in the Biomarker Details for variants.
To display the date in IGV, perform one of the following actions:
To view data at the variant level, select the IGV column entry for the variant.
To view data at the case level, select Case Visualization above the grid. The IGV visualization is displayed in a new browser tab.
To display the data for a local file, select Local File, and then navigate to an IGV-formatted file.
To display the genome sequence data, select UCSC Genome Browser.
❗ Large visualization files must be compressed before upload.
To view reference tracks, select IGV Track Settings, and then select the checkboxes for the tracks or group of tracks you want to view.
[Optional] View break ends. The breakend view zooms in on the ends of the breakpoints in the sequence.
To visualize breakends in separate views, select View Breakends.
To return to a single breakend view, select Join Breakends.
[Optional] Select Add New Comment to add or update a comment about the variant. Each new or updated IGV comment is copied as a separate entry to the Variant Details tab comments for the variant.
❗ The Variant Details tab does not indicate the source of the comments. To differentiate entries created in IGV, preface comments with IGV or another short identifier.
Use the following options to interact with the visualization:
Zoom into an area of interest.
Pan the visualization by clicking and dragging or by selecting the left and right arrows on the karyogram.
Select an item in the visualization to view additional information about the item.
Show or hide IGV elements.
Karyotype Panel
Track Labels
Center Line
Cursor Guide
Change the track settings.
Set track name.
Set track height.
Collapse, squish, or expand exon rows.
Remove track.
❗ The gene model display track reflects the transcript reference standard (Ensembl or RefSeq) specified in Settings.
Column | Description |
externalid | An optional external reference ID that can be used to trace the assertion back to your system. |
type | A required field that specifies the assertion type. Acceptable values are as follows. • Biological • Therapeutic • Prognostic • Diagnostic • Predictive • Gene Information |
classificationName |
classificationOrder |
classificationBackgroundColor |
direction | A required field for Therapeutic and Prognostic that specifies the direction of the assertion. Acceptable values are as follows. For Therapeutic: • Responsive • Non-responsive • Contraindicated For Prognostic: • Favorable • Unfavorable |
status | A required field for TMB, MSI, and GIS assertions Acceptable values are as follows. • High • Low |
hrd | A required field. Acceptable values are as follows. • Undetermined • Positive • Negative When interpreting biomarkers in a case, this information is visible for BRCA1/2 variants andGIS. |
geneRoles | An optional field used for the gene description assertion. Acceptable values are as follows. • Oncogene • Tumor Suppressor • Oncogene / Tumor Suppressor |
summary | An optional field where an interpretation summary can be added. You can specify up to30,000. characters. This information is included in PDF reports. |
notes | An optional field where interpretation notes can be added. You can specify up to 30,000characters. This information is not included in PDF reports. |
diseaseName | An optional field that specifies the disease name. The system can determine the name based on the diseaseOntology and diseaseOntologyId provided. |
diseaseOntology |
diseaseOntologyID | A required field that specifies the disease ontology ID. |
therapy | A required field for Therapeutic that specifies the therapy. Multiple drug names can bespecified by separating them with a pipe. |
biomarkerType | A required field that specifies the type of biomarker the assertion is for. • Acceptable values are as follows. • Small variant • Copy number variant • Structural variant • RNA splice variant • RNA fusion variant • Genomic analysis (ie, TMB, MSI, GIS) |
variantType | A required field for Copy number variant and Structural variant. Acceptable values are as follows. For Copy number variant: • Copy number variation • Copy number loss • Copy number gain • Copy number neutral For Structural variant: • Tandem duplication • Insertion • Deletion • Inversion • Translocation |
level | A required field that specifies the curation level. Acceptable values are as follows. For Small variants: • Nucleotide • Amino Acid • Codon • Exon • Gene For Copy Number variants: • Annotation overlap • Gene For Structural variants: • Annotation overlap, if variant type is not Translocation • Partial fusion • Exact fusion For RNA splice variants: • Annotation overlap • Exon For RNA fusion variants: • Partial fusion • Exact fusion For Genomic analysis: • TMB • MSI • GIS |
genomeBuild | A required field that specifies the genome build. Acceptable values are as follows. • 37 • 38 |
chromosome | A required field for levels nucleotide and annotation overlap that specifies the chromosome. Acceptable values are as follows. • 1–22 • X • Y • MT |
position | A required field for levels nucleotide and annotation overlap that specifies the VCF position. Acceptable values are within the chromosome range. |
end | A required field for level annotation overlap that specifies the VCF end position. Acceptable values are within the chromosome range. |
ref | A required field for level nucleotide that specifies the VCF reference allele. Acceptable values are combinations of A, T, C, G. |
alt | A required field for level nucleotide that specifies the VCF alternate allele. Acceptable values are combinations of A, T, C, G. |
transcriptId | A required field for the following curation levels that specifies the transcript ID. • Nucleotide • Amino acid • Codon • Exon Acceptable values are RefSeq and Ensembl transcript IDs, with or without the version. |
codon | A required field for level codon that specifies the codon. Acceptable values are a three-letter hgvsp abbreviation, including prefix “p.(“ and suffix “)” and without the amino acid change, such as p.(Val600). Only missense variants aresupported. |
hgvsp | A required field for level amino acid that specifies the hgvsp. Acceptable values are a three-letter hgvsp abbreviation, including prefix “p.(“ and suffix “)”, such as p.(Val600Glu). |
exon | A required field for level exon that specifies the exon. The acceptable value is [exon #]. |
geneSymbol | A required field. If the NCBI gene ID is not provided, then the following levels specify thegene symbol: • Gene • Partial fusion • Exact fusion |
ncbiGeneId | A required field. If the gene symbol is not provided, then the following levels specify the NCBIgene ID: • Gene • Partial fusion • Exact fusion |
fusionGeneSymbol | A required field for level exact fusion. If the fusion NCBI gene ID is not provided, this fieldspecifies the fusion gene symbol. |
fusionNcbiGeneID | A required field for level exact fusion. If the fusion gene symbol is not provided, this fieldspecifies the fusion NCBI gene ID. An optional field for level partial fusion. |
fusionPosition | An optional field for levels partial fusion and exact fusion that specifies the fusiondirectionality. Acceptable values are 0 and 1. • Without a value, the fusion directionality is unspecified, such as EML4/ALK. • If 0 is provided, the fusion is at position 0, such as [fusion gene]-[gene]. • If 1 is provided, the fusion is at position 1, such as [gene]-[fusion gene]. |
consequence | An optional field for levels exon and gene that specifies the consequence. When a consequence is specified, the assertion only matches to a case variant that has heconsequence specified, such as EGFR exon 19 inframe deletion. Acceptable values are the following sequence ontology values: For small variant, exon level: • 3_prime_UTR_variant • 5_prime_UTR_variant • coding_sequence_variant • downstream_gene_variant • frameshift_variant • inframe_deletion • inframe_insertion • intron_variant • mature_miRNA_variant • missense_variant • NMD_transcript_variant • non-coding_transcript_exon_variant • non-coding_transcript_variant • protein_altering_variant • splice_acceptor_variant • splice_donor_variant • splice_region_variant • stop_retained_variant • synonymous_variant • upstream_gene_variant For small variant, gene level: • start_lost • stop_gained • stop_lost • incomplete_terminal_codon_variant • feature_elongation • feature_truncation • splice_donor_variant • splice_acceptor_varian • splice_region_variant • frameshift_variant • inframe_deletion • inframe_insertion • missense_variant • protein_altering_variant • coding_sequence_variant • upstream_gene_variant • downstream_gene_variant • intron_variant • 5_prime_UTR_variant • 3_prime_UTR_variant • non-coding_transcript_exon_variant • non-coding_transcript_variant • synonymous_variant • start_retained_variant • stop_retained_variant • mature_miRNA_variant • NMD_transcript_variant • regulatory_region_ablation • regulatory_region_amplification • regulatory_region_variation For copy number variant, gene level: • copy_number_decrease • copy_number_increase • copy_number_change For RNA splice variant, exon level: • exon_loss_variant |
Connected Insights performs variant annotation and matches variants to the records in external knowledge bases and functional impact predictions based on a set of pre-selected default transcripts. Variant details, such as c.HGVS and p.HGVS labels and consequences, are also generated based on default transcripts.
In the current implementation, you can only change transcripts for specific variants.
View default transcripts as follows.
Add the Transcript column in the variant grid of the Variants page. The HGVS and Consequences columns provide variants c.HGVS and p.HGVS labels and consequences based on the default transcript. Selecting More in the Consequences column shows all consequences for the default transcript (left column) and all transcripts including the default one (right column).
Open the Biomarker Details page by selecting Interpret on the Overview or Variants page. The default transcript is provided in the top-right corner. A ☆ represents the default transcript, while a C represents the canonical transcript
In Connected Insights, the following rules determine the default transcript:
If there are preferred transcripts annotated for the given report, limit to the list of preferred transcripts for a given variant. If there are no preferred transcripts for the given variant, skip this step.
When present, limit to the collection of transcripts for a given variant that have assertions from any source. This step prioritizes transcripts by highest assertion actionability, then by the most specific assertion level.
Limit to the collection of transcripts for a given variant that are the highest tier by consequence based on the variant category.
If canonical transcripts are present, limit to canonical transcripts.
Limit to the genes in the key genes configuration for the case disease.
When present, limit to the genes that have the highest role classification from Cancer Gene Census (Oncogene > Fusion > TSG).
Select the gene that is first alphabetically.
If RefSeq and Ensembl transcripts are present, limit to RefSeq transcripts.
If there are multiple transcripts remaining, select the first transcript alphabetically.
Assertions include the following levels:
Nucleotide
DNA
Amino Acid
Codon
Exon
Exact Fusion
Annotation Overlap
Gene
Partial Fusion
The following variant categories define consequence tiers:
In the current version of Connected Insights, users can only change transcripts for specific variants. The transcripts can be viewed and updated in the top-right corner of the Biomarker Details page for a specific variant. Changing transcripts updates the information for this variant in the variant grid and in the Biomarker Details page content. These updates include assertions in the following sections that have transcript-specific content:
My Knowledge Base
Other Knowledge Bases
Clinical Trials
Computer Predictors
The variant grid can be found under the Variants tab within a case. Each tab represents a filtered list of the variants and each row contains data for one variant. The data include biological information associated with the variant in various annotation sources. The variant grid provides a set of tools to sort,filter, flag, and review variants.
By default, the page displays a list of variants that meet the criteria of the filter configured in the test definition. Adding new filters creates additional tabs,with each having a list of variants meeting the criteria of the corresponding filters. For more information about applying filters, refer to .
The following table lists the contents of each column in the variant grid.
Variant interpretation refers to understanding biological significance of the variants and recording it by assigning pathogenicity and/or actionability categories. To view variant information, open a case and select the Variants tab.
The exact interpretative actions are different between laboratories and depend on the type of test, report template, and specifics of the given case. Typically, user actions include the following steps:
Open the case from the case list and review the subject information for the case.
Select the Variants tab to display the variant grid for review and interpretation. a. Customize variant information displayed in the variant grid. For more information, refer to . b. Apply or modify variant filters. For more information, refer to . c. Review variant quality using the Integrative Genomics Viewer (IGV). For more information, refer to . d. Flag the variant as needed to support communication between variant reviewers. For more information, refer to .
View more information about the variant.
Create variant assertions and include the selected variants in the report. For more information, refer to .
The Lab QC tab within a case provides basic assay, workflow, and output metrics. If a case was created from merging DNA and RNA, then DNA and RNA tabs are selectable before the Overview section.
Run QC Metrics displays metrics used for the run as specified in the uploaded metrics file.
Sample QC Metrics displays metrics used for the sample as specified in the uploaded metrics file.
The Overview tab displays a high-level view of the most relevant variants in the case. This tab contains a list of genes and shows variants detected in that case within those genes. The variants in this list are filtered according to the filter that was selected as part of the test definition. The key genes are predefined by Connected Insights based on cancer type.
The Lab QC section provides an overview of the following information contained under the Lab QC tab:
Metric
Value
Status (Pass/Fail)
For more information on configuring metrics that display in the Lab QC section and their thresholds, refer to .
View the % Estimated Tumor Purity and Estimated Tumor Ploidy in the Overview tab. This information displays under Tumor Characteristics.
The following biomarkers provide an overview of the measurable biological markers. The content in these fields comes from secondary analysis files and is displayed here.
Tumor Mutational Burden (TMB) — Displays the TMB in mut/MB. The TMB section also shows TMB-Low and TMB-High statuses.
Microsatellite Instability (MSI) — Displays the MSI as a percentage. The MSI section also shows MS-Stable and MSI-High statuses.
Genomic Instability Score (GIS) — Displays the GIS. The GIS section also shows GIS-Low and GIS-High statuses.
This section provides information on genes specific to the disease, gene coverage, and variants.
Genes Specific to the Disease
Gene Coverage
Gene coverage tracks show the following data in a graph:
Gene coverage — The Y-axis indicates the gene coverage (for example, 50X).
Hotspots — Hotspots are plotted along the X-axis and are derived from the Cancer Hotspots website.
Variants
Variants for each gene are shown with My Knowledge Base and Other Knowledge Base assertions.
My Knowledge Base assertions include the following classifications:
Highest biological classification across all diseases
Highest actionability classification for therapeutic classifications across case and ancestor diseases
Highest actionability classification for prognostic classifications across the case and ancestor diseases
Diagnostic classifications across all diseases Other Knowledge Base assertions include the following classifications and filters:
Highest actionability classifications for JAX-CKB and CIViC, including: – Therapeutic classifications across case and ancestor diseases – Prognostic classifications across the case and ancestor diseases – Diagnostic classifications across all diseases
The variant grid provides a configurable view of variants in a case. You can create new filtered views and customize the column configuration in the grid.
The configured view applies only to the selected case.
Modifying how data appear in the variant grid only affects how information is arranged in the table. Modifying views does not change the underlying data.
The test definition specifies one or more default tabs that provide filtered variant views. Each view resides on a different tab with a unique set of filters. The tab lists the name of the filter and the number of variants passing the filter. Refer to to learn how to create and modify variant filters.
You can create an unlimited number of tabs for as many additional views as necessary.
Show, hide, and reorder columns in the grid for a custom view of data in the tab. Changing the column order changes the view for all users.
Drag a column to move it.
Columns with additional data can be expanded by selecting (+More).
Select the menu next to the column name and change any of the following options: – Show or hide columns. – Pin a column. – Resize columns.
The Interpret, Flag, and IGV columns in This Case section are always visible and cannot be hidden or moved.
Column configurations can be saved to appear in the same order for every case. Column configurations are saved together with a filter as part of the tab in the variant grid.
Show, hide, and organize columns as desired. If filtering logic is focused on a certain variant category, columns could be configured to view data relevant to that variant category.
Select Edit Variant Filters.
Select Save As.
Use the filter and column configuration for other cases by loading the filter or by adding the filter to default filters in Test Definitions.
The variant grid default sort is by the actionability category of variants interpreted in past cases, followed by COSMIC. Each tab can support a different custom sort that includes up to 10 columns. Custom sort configuration is per-tab and persists across sessions.
An arrow in the column heading indicates that the column is sorted. If more than one column is sorted, a number indicates the sort level.
To sort a column, select the column heading.
To add a level of sort, hold the shift key and select a different column heading. Select the heading again to reverse the sort for the column.
To clear the sort, select any column without holding the shift key.
This page summarizes filters related to variant – disease and gene – disease associations. Filter availability can vary depending on the selected variant categories. If filters are applied to more than one variant category in the same condition group, only filters relevant for all variant categories are available. For more information, refer to .
In addition to filtering by the gene list, variants can be filtered by genes based on their associations with diseases and phenotypes.
Select the genes filter.
In the displayed dialog box window, select the Include genes from the diseases checkbox.
Start typing a phenotype or disease to display a list of potential matches to add to the list.
Select a checkbox next to Resource to include it in the list.
Select a high, medium, or low confidence score.
Select an overlap distance between 0.00 and 1.00.
The disease and related diseases display in the Related Diseases area with the distance and gene count. Deselect any unnecessary related diseases.
Add any other genes to the gene list.
Add additional genes in the Additional genes area.
Select Apply to save changes to the gene list.
The following tables detail the ontology sources that Connected Insights uses to determine relationships between genes and diseases.
Phenotype to gene search finds similar phenotypes and diseases across various ontology sources, independent of the underlying vocabulary in each source. If an equivalent concept does not exist across the sources, Connected Insights calculates the distance between nodes in the ontological hierarchies and assigns a score from 0 to 1, where:
Values closer to 0 indicate that the concepts are more equivalent. A value of 0 indicates that the concepts are the same.
Values closer to 1 indicate that the concepts are more dissimilar. A value of 1 indicates that the concepts can only be connected at the root node and are therefore excluded from query results.
The determination of distance accounts for the fact that sibling concepts on leaf nodes (eg, hypertrophic cardiomyopathy, and dilated cardiomyopathy) are more closely related to each other than siblings close to the root (eg, abnormal vascular morphology, and abnormal heart morphology).
Confidence scores for gene - disease associations are calculated using the following rules:
Expert-curated data from OMIM, HPO, Phenopedia, and ClinVar are assigned a high confidence score.
High, moderate, or low confidence scores are converted from GeL PanelApp strong, medium, and low scores, respectively.
GTR confidence scores are based on information content metrics, which measure the specificity of a genetic test for a particular phenotype and a gene.
GeneRIF associations, which are derived using data mining, and assigned medium confidence.
Filters variants based on gene role in cancer annotated by COSMIC Cancer Gene Census (CGC).
Filters variants based on genes with known gene-disease associations in the OMIM database.
Present in OMIM — An OMIM entry exists for the gene.
Has associated OMIM phenotypes (including ?) — A relationship exists between the phenotype and a matching gene at the transcript level. Provisional relationships, indicated by "?" in OMIM, are included.
Has associated OMIM phenotypes (excluding ?) — A relationship exists between the phenotype and a matching gene at the transcript level. Provisional relationships, indicated by "?" in OMIM, are excluded.
Selecting associated phenotypes enables options to refine the filter by mode of inheritance.
❕ The COSMIC filter is only selectable for small variants.
Filters by number of samples in cancer hotspots.
Filters on interpretation categories and the review status provided in the ClinVar database.
To filter by ClinVar review status, use the definitions provided from the ClinVar status review guidelines on the National Center for Biotechnology Information website.
This page summarizes filters related to the functional impact of a variant. Filter availability can vary depending on the selected variant categories. If filters are applied to more than one variant category in the same condition group, only filters relevant for all variant categories are available. For more information,refer to .
Filters by gnomAD constraint metrics: LOEUF, misZ, pLI, misZ, pLI, pNull, pRec, and synZ. For more information, refer to .
Filters by the haploinsufficiency and triplosensitivity evidence classification. It represents the strength of evidence supporting a relationship between a gene and disease and whether loss (haploinsufficiency) or gain (triplosensitivity) of individual genes or genomic regions is a mechanism for disease(Riggs et al., Clin Genet. 81, 403–412 (2012)).
The evidence categories can be used for clinical interpretation of copy number variants using the categories recommended by ClinGen.
This page summarizes filters related to variant quality. Filter availability can vary depending on the selected variant categories. If filters are applied to more than one variant category in the same condition group, only filters relevant for all variant categories are available. For more information, refer to .
Filters data by the value provided for the variant in the FILTER column of the VCF file. Refer to the variant caller documentation to confirm possible values and recommended thresholds.
Filters data by read metrics, for example, VAF, allele depth, paired and read counts, split read count, and others.
Excludes small variants in low complexity regions (LCRs).
For more information, refer to .
This page summarizes filters related to variant details. Filter availability can vary depending on the selected variant categories. If filters are applied to more than one variant category in the same condition group, only filters relevant for all variant categories are available. For more information, refer to .
Filters variants by Suspected Somatic or Predicted Germline origin.
You can select these options when creating or editing a variant filter by updating the Origin criterion. For example, if you do not want predicted germline variants, then add or update the Origin criterion to only include Suspected Somatic. For more information, refer to .
You can also add or edit a test definition to include either somatic or predicted germline variants through selecting the applicable variant filters in the Variant Filter(s) field. For more information, refer to .
For tumor-only analyses, when enabled in DRAGEN, variant origin is determined for small variants based on population frequency databases.
For tumor-normal analysis, when enabled in DRAGEN, variant origin is determined for small variants based on the presence or absence of the variant in the normal sample.
Filters small variants by overlap with an LOH event when LOH data is provided.
Filters variants by genes. There are two ways to create gene lists in the filter.
Using a list of gene names. To create a gene list, type or paste gene names in the Additional Genes field.
Using gene-disease associations from several sources. For more information, refer to .
Filters small variants, structural variants, and copy number variants by their types.
❗ The variant type is only selectable in a filter group with a single selected variant category as the variant types are tied to specific variant categories.
Filters data by specific consequences.
❗ The consequence filter is only selectable in a condition group with a single selected variant category as the consequences are tied to specific variant categories.
When annotating transcripts with terms, Connected Insights uses the most specific term supported by the variant annotator.
Consequence filters return only the specified term and do not automatically include child terms. Specify the exact terms to include in the filter results.
These consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, JAX-CKB or MyKnowledge Base).
Start and Stop Alterations
Filters data by the presence and location of start and stop alterations.
Splice Site
Filters data by the affected splice site.
Indels
Other
Filters data by the variant relationship to a gene.
When annotating transcripts with terms, Connected Insights uses the most specific terms supported by the variant annotator. Consequence filters return only the specified term and do not automatically include child terms. Specify the exact terms to include in the filter results.
These consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, JAX-CKB or MyKnowledge Base).
Filters data by the transcript consequence.
Filters data by the gene fusion consequence.
When annotating transcripts with terms, Connected Insights uses the most specific term supported by the variant annotator. Consequence filters return only the specified term and do not automatically include child terms. Specify the exact terms to include in the filter results.
These consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, JAX-CKB or MyKnowledge Base).
Filters data by the transcript consequence.
Filters data by the copy number consequence.
The functional consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, JAX-CKB or My Knowledge Base).
The functional consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, CKB or My Knowledge Base).
Filters by specified chromosomes. If no chromosome is selected, the chromosome filter is not applied.
Filters by specified regions. The input format is chr#: start-stop
, within multiple regions separated by spaces or new lines.
These values indicate a reference, deletion, or amplification of copy number variants.
❗ The change (copy number) filter is only selectable in a condition group with only the copy number variant category.
With copy number variants, the fold change value is derived from the normalized read depth of the gene in a sample. This depth is relative to the normalized ready depth of diploid regions in the same sample.
❗ The change (fold change) filter is only selectable in a condition group with only the copy number variant category.
Filters data by variant length with resolution up to one bp.
Variants filters provide options for applying any combination of inclusion and exclusion criteria to the variants in a case. Filter criteria can vary depending on the selected variant categories. If filters are applied to more than one variant category in the same filter group, only filters relevant for all variant categories are available. For more information, refer to .
Each filter combination resides on a different tab in the variant grid. Default filter views are defined in the test definition. You can create filter tabs in the grid for as many additional views as necessary. Filters applied in the variant grid are specific to the selected case.
For more information about filter options, refer to and
When you configure a new test, you can add one or more specific filters to the test definition. The filters become default filters and are applied to every case in your workgroup. The default filters are locked and shown in the first tabs of the variant grid. For more information, refer to .
The default filter tabs, indicated by a lock, cannot be altered or deleted for the cases already processed. To change or delete default filters, you must update the filters that are used in the test definition and reprocess the case and upcoming cases through the updated test definition.
Included with Connected Insights, a demonstration of the filtering is provided as a template for you to define your own filter views. In the primary filter group, the filter is set up to return all variants categories (ie small variants, copy number variants, structural variants, RNA fusion variants, and RNA splice variants) and requiring that these are called with a PASS
by each of the variant callers. In the subsequent filter groups, the filter is set up to apply the following logic for each of the variant categories:
Small variants with coding consequences and population frequency ≤ 0.05 in gnomAD for AFR, AMR, EAS, NFE, SAS
Any copy number variants
Structural variants resulting in a unidirectional gene fusion with at least three supporting reads
RNA fusion variants resulting in a unidirectional gene fusion
RNA splice variants resulting in an exon loss
Configure and modify case-specific filter views in new or unlocked variant grid tabs. The default filter tabs, indicated by a lock, cannot be altered or deleted.
Create a tab using one of the following methods:
To create a filter, select New Filter.
To copy an existing filter, select the tab drop-down arrow and then select Duplicate Filter.
To load a new filter, select Load Filter.
Select or search for a filter to load from the list of compatible filters created and saved by all users in your workgroup. Filters with variant flags are only compatible to the cases using the same flag list. Select Apply.
[Optional] Double-click the tab label and enter a new name.
Select Edit Variant Filters.
Select Apply.
To lock a filter view, select the tab drop-down arrow, and then select Lock Filter. Locked filter views are indicated by a blue lock and cannot be deleted.
To edit a filter name, select the tab drop-down arrow, and then select Edit Filter Name.
After editing the name, select Save.
To save a filter view, select Edit Variant Filters, then select Save As. The filter is saved and can be configured in the test definitions to be a default filter and be used across cases. Column configurations and filter dependencies are saved with the filter.
To remove a filter view, delete the tab. Default tabs are indicated by a lock and cannot be deleted.
Export a list of variants and variant data to a tab-delimited file.
The maximum number of exported variants in a list is 7500. If the list exceeds the maximum, only the first 7500 results are included in the exported file.
Configure the filters and flags to show only the variants to export.
Select the tab drop-down arrow, and then select Export Grid as TSV.
Connected Insights includes the Flags filter that filters variants by the custom flags defined in Test Components. For more information, refer to
Clinical trials are listed in this when one of the knowledge bases determines the trial to be a match for the variant. The information in this table is from the clinical trial database.
By default, the assertions are filtered by the case and ancestor diseases. Ancestor diseases are determined using SNOMEDCT. These diseases can be viewed at the , with the following exceptions:
Descendents of neoplastic disease do not include ancestors beyond neoplastic disease.
Non-small cell lung cancer has been added as an ancestor of adenocarcinoma of lung.
You can also filter by other diseases, title, city, state, and country.
Filter changes are saved and applied across variants within a case and can be reset if needed.
Connected Insights provides access to the National Library of Medicine Clinical Trials website, which provides information on publicly and privately supported clinical studies on a wide range of diseases and conditions.
The following from JAX-CKB are not currently supported:
Clinical trials with a recruitment status of completed, withdrawn, or active, not recruiting.
Variants that have the excluded requirement type.
The software does not yet determine if a case has all the requirements for a clinical trial (for example, a clinical trial requires two variants).
The Biomarker Details page brings together key information and actions related to variants. The page exists for individual variants and genome-wide biomarkers like TMB and MSI. You can use the Biomarker Details page to do the following:
Interpret the variant and include it in the report.
Review assertions already created for the variant. For more information, refer to .
Review sign-off reports that included the variant. For more information, refer to .
Review variant information related to oncology: – Knowledge bases. For more information, refer to . – Clinical trials. For more information, refer to .
Review variant information. For more information, refer to Variant Overview. – Annotation details – Gene information – Records in external sources – Functional impact predictions – Population frequency
Set gene transcripts. For more information, refer to .
To open the Biomarker Details page, select Interpret for a specific variant in the Overview or Variants tab.
A required field that specifies the assertion classification. Examples are as follows. For Biological: • Pathogenic • Likely Pathogenic • Uncertain Significance • Likely Benign • Benign For Therapeutic, Prognostic, Diagnostic: • Tier 1A • Tier 1B • Tier 2C • Tier 3 • Tier 4 When interpreting biomarkers in a case, the default values are the same as the examples. In the Configuration screen, you can customize and set the prioritization of these values. We recommend using the same classification here and in the Configurations screen. For moreinformation, refer to
A required field that specifies the assertion classification. Examples are as follows. For Biological: • For Pathogenic, 1.0 • For Likely Pathogenic, 2.0 • For Uncertain Significance, 3.0 • For Likely Benign, 4.0 • For Benign, 5.0 For Therapeutic, Prognostic, Diagnostic: • For Tier 1A, 1.0 • For Tier 1B, 2.0 • For Tier 2C, 3.0 • For Tier 2D, 4.0 • For Tier 3, 5.0 • For Tier 4, 6.0 When interpreting biomarkers in a case, the default values are the same as the examples. In the Configuration screen, you can customize and set the prioritization of these values. We recommend using the same classification here and in the Configurations screen. For moreinformation, refer to When multiple classifications map to the same AMP/ASCO/CAP tier, increment the tenthsvalue For example, if Level 1 and Level 2 both map to Tier 1A, the classificationOrder is as follows: • Level 1, 1.0 • Level 2, 1.1
A required field that specifies the assertion classification. Examples are as follows. For Biological: • For Pathogenic, red • For Likely Pathogenic, pink • For Uncertain Significance, yellow • For Likely Benign, light green • For Benign, green For Therapeutic, Prognostic, Diagnostic: • For Tier 1A, red • For Tier 1B, red • For Tier 2C, violet •or Tier 2D, violet • For Tier 3, blue • For Tier 4, green When interpreting biomarkers in a case, the default values are the same as the examples. In the Configuration screen, you can customize and set the prioritization of these values. We recommend using the same classification here and in the Configurations screen. For moreinformation, refer to
A required field that specifies the disease ontology. We currently recommend using SNOMEDCT. The SNOMEDCT ID can be found by navigating to an existing case and searching for the disease in the Case Details or assertion form. The ID can also be found by using the International Edition browser at the .
For more information on setting thresholds for the statuses, refer to .
Select Interpret to open the biomarker details. For more information, refer to .
For more information on how to set up genes specific to the disease, refer to .
Transcript exons and introns — Transcript is the preferred transcript (if specified) or the RefSeq transcript. For more information on specifying a preferred transcript for a gene, refer to .
Variants — Variants in the gene that pass default filters. For more information on how to set up a default filter, refer to .
Default filters that show the variant To interpret variants from the Overview tab, select Interpret. For more information, refer to .
Filters by presence in the COSMIC database. For more information, refer to .
Filters by the SpliceAI score. For more information, refer to .
Filters by the PrimateAI-3D score. For more information, refer to .
Build and edit variant filters by applying various filtering criteria to the gene and variants. For more information, refer to .
VariantCategory | Consequence Tier 1 | Consequence Tier 2 | Consequence Tier 3 | Consequence Tier 4 | Consequence Tier 5 | Consequence Tier 6 |
Small Variant | • Gain of Function • Loss of Function | • Start Loss •Stop Gained • Stop Loss • Feature Truncation • Frame shift Variant • Splice Donor Variant • Splice Acceptor Variant | • Incomplete Terminal Codon • Feature Elongation • Splice Region Variant • Inframe Deletion • Inframe Insertion • Missense Variant • Protein Altering Variant • Coding Sequence Variant | • Intron Variant • 5' UTR Variant • 3' UTRVariant • Noncoding Transcript Exon Variant • Noncoding Transcript Variant • Synonymous Variant •Start Retained Variant • Stop Retained Variant •NMD Transcript Variant | • Upstream Gene Variant • Downstream Gene Variant • Mature miRNA Variant • Regulatory Region Ablation • Regulatory Region Amplification • Regulatory Region Variation •Any other undefined transcript consequences |
Copy NumberVariant (CNV) | • Gain of Function • Loss of Function | • Copy Number Decrease • Loss of Heterozygosity | • Copy Number Increase • Copy Number Change | • Transcript Ablation • Feature Truncation • Feature Elongation | • Transcript Amplification •Transcript Variant • 5' Duplicated Transcript • 3' Duplicated Transcript | Any other undefined transcript consequences |
Structural Variant or RNAFusion Variant | • Gain of Function • Loss of Function | • Unidirectional Gene Fusion | • Bidirectional Gene Fusion • Gene Fusion | • Transcript Ablation • Feature Truncation • Feature Elongation | • Transcript Amplification •Transcript Variant • 5' Duplicated Transcript • 3' Duplicated Transcript | Any other undefined transcript consequences |
RNA Splice Variant | •Gain of Function •Loss of Function | Exon Loss Variant | Any other undefined transcript consequences |
Field Name | Description |
Source | Description |
Assay | The name of the assay as specified in the uploaded metrics file. |
Output Date | The output date of the run as specified in the uploaded metrics file. |
Output Time | The output time of the run as specified in the uploaded metrics file. |
Workflow Version | The workflow version of the run as specified in the uploaded metrics file. |
Module Version | The module version of the run as specified in the uploaded metrics file. |
Run ID | The ID of the run as specified in the uploaded metrics file. |
Run Name | The name of the run as specified in the uploaded metrics file. |
Field Name | Description |
Source | Description |
Metric | Metrics used for the run as specified in the uploaded metrics file.Examples include total percentage of reads passing filter and Q30 scores. |
Lower Spec Limit | Lower specification limit for metric as specified in the uploaded metrics file. |
Upper Spec Limit | Upper specification limit for the metric as specified in the uploaded metrics file. |
Value | The value of the metric as specified in the uploaded metrics file. |
Pass Status | Indicates whether the metric passed the spec limits as specified in the uploaded metrics file. |
Field Name | Description |
Source | Description |
Section | The section for each set of metrics as specified in the uploaded metrics file. Examples include DNA sample QC and RNA sampleQC. |
Group | The group for the metrics as specified in the uploaded metrics file(for example, read group). |
Metric | Metrics used for the sample as specified in the uploaded metrics file. Examples include median exon coverage and median fragment length. |
Lower Spec Limit | Lower specification limit for the metric as specified in the uploaded metrics file. |
Upper Spec Limit | Upper specification limit for the metric as specified in the uploaded metrics file. |
Sample/Pair ID | The sample/pair ID of the case. |
File Type | Sample File Name | Field |
JSON | *.tmb.json | {"TmbPerMb": 3.15823318} |
CSV | *.tmb.metrics.csv | TMB, 5.51 |
File Type | Sample File Name | Field |
JSON | .gis.json | { "MYRIAD": { "score": { "GIS": "3" } } } |
File Type | Sample File Name | Field |
JSON | .msi.json | { "PercentageUnstableSites": 3.19 } |
Resource | Description |
OMIM | Online Mendelian Inheritance in Man |
HPO | Human Phenotype Ontology |
Phenopedia | Human Genome Epidemiology (HuGE) |
GEL PanelApp | Genomics England PanelApp |
ILMN | • Clinvar – NCBI ClinVar •MedGen – NCBI portal to information about conditions and phenotypes related to Medical Genetics. •GTR – NCBI Genetic Testing Registry •GeneRIF – NCBI Gene Reference into Function |
Resource | Description |
ICD-9 | International Classification of Diseases, Ninth Revision |
ICD-10 | International Classification of Diseases, Tenth Revision |
MeSH | Medical Subject Headings |
UML | Unified Medical Language system. A repository of ontology resources. |
SNOMEDCT | Systematized Nomenclature of Medicine Clinical Terms |
Role in Cancer | Description |
TSG | Known tumor suppressor gene (TSG). |
Oncogene | Known oncogene. |
Fusion | Known fusion gene. |
Mode of Inheritance | Description |
AD | Autosomal Dominant |
AR | Autosomal Recessive |
XL | (X-linked) |
XLD | (X-linked Dominant) |
XLR | (X-linked Recessive) |
YL | (Y-linked) |
MI | Mitochondrial |
Mu | Multifactorial |
DD | Digenic Dominant |
DR | Digenic Recessive |
SMu | Somatic Mutation |
SMo | Somatic Mosaicism |
IC | Isolated Cases |
Interpretation Category | Definition in Connected Insights |
Pathogenic | The variant has at least one aggregate variant record (VCV entry) or aggregate variant –disease record (RCV) with classification category Pathogenic in the ClinVar database. |
Likely Pathogenic, UncertainSignificance, Likely Benign, Benign | The variant has at least one aggregate variant record (VCV entry) or aggregate variant –disease record (RCV) with classification category Pathogenic in the ClinVar database. |
None | The variant has no records in ClinVar or has at least one aggregate variant record (VCV entry)or aggregate variant – disease record (RCV) with interpretation categories Drug Response,Protective, and others (any other categories excluding Pathogenic, Likely Pathogenic,Uncertain Significance, Likely Benign, and Benign). |
Number of Stars | Definition in Connected Insights | Review Status Descriptions |
Four | The highest review status across all VCV and RCV records for the variant is four stars. | Practice guideline. For more information,refer to the ClinVar status review guidelines on the National Center for Biotechnology Information website. |
Three | The highest review status across all VCVand RCV records for the variant is three stars. | Reviewed by export panel. For more information, refer to the ClinVar status review guidelines on the National Center for Biotechnology Information website. |
Two | The highest review status across all VCVand RCV records for the variant is two stars. | Criteria provided, multiple submitters, no conflicts. Two or more submitters with assertion criteria and evidence (or a public contact) provided the same interpretation. |
One | The highest review status across all VCV and RCV records for the variant is one star. | Criteria provided, conflicting interpretations. Multiple submitters provided assertion criteria and evidence(or a public contact) but there are conflicting interpretations. The independent values are enumerated for clinical significance. |
None | The highest review status across all VCV and RCV records for the variant is no stars. | No assertion criteria provided. For more information, refer to the ClinVar status review guidelines on the National Center for Biotechnology Information website. |
Consequence | Description |
Gain of Function Variant | The variant results in gain of function. |
Loss of Function Variant | The variant results in loss of function. |
Consequence | Description |
Start Loss | The loss of a start codon in the coding sequence. |
Stop Gained | The gain of a stop codon in the coding sequence. |
Stop Loss | The loss of a stop codon in the coding sequence. |
Incomplete Terminal Codon | A change to at least one base of the final codon of an incomplete annotated transcript. |
Feature Elongation | The variant causes the extension of the genomic feature. |
Feature Truncation | The variant causes the reduction of a genomic feature. |
Type | Description |
Splice Acceptor Variant | The variant affects the canonical splice acceptor site (last two bases of the 3' end of the intron). |
Splice Donor Variant | The variant affects the canonical splice donor site (first two bases of the 5' of the intron). |
Splice Region Variant | An indel or substitution in a non coding splice region of the gene. |
Type | Description |
Frameshift Variant | An insertion or deletion in which the number of base pairs is not divisible by 3, causing a frame disruption. |
Inframe Deletion | A deletion that does not disrupt the reading frame. |
Inframe Insertion | An insertion that does not disrupt the reading frame. |
Type | Description |
Missense Variant | A single base pair substitution that results in the translation of a different amino acid at the position. |
Protein Altering Variant | The variant has a protein-altering coding consequence. |
Coding Sequence Variant | The variant changes the coding sequence. |
Type | Description |
Intergenic Variant | The variant position is not covered by any gene transcript. |
Upstream Gene Variant | The variant position is within 5 kb upstream of the defined transcript start coordinate. |
Downstream Gene Variant | The variant position is within 5 kb downstream of the defined transcript end coordinate. |
Intron Variant | The variant occurs within an intron region. |
3-prime UTR Variant | The variant is in the 3' untranslated region of a gene. |
5-prime UTR Variant | The variant is in the 5' untranslated region of a gene. |
Noncoding Transcript Exon Variant | The variant changes the noncoding exon sequence in a noncoding transcript. |
Noncoding Transcript Variant | The variant occurs in a noncoding RNA gene. |
Synonymous Variant | The variant does not affect the primary amino acid sequence of the translated protein. |
Start Retained Variant | At least one base in the start codon is changed, but the start codon remains. |
Stop Retained Variant | At least one base in the terminator code is changed, but the terminator remains. |
Mature miRNA Variant | The variant occurs within a mature miRNA sequence. |
NMD Transcript Variant | The variant is in a transcript and is the target of nonsense-mediated decay (NMD). |
Regulatory Region Ablation | A deletion of a region that contains a regulatory region. |
Regulatory Region Amplification | An amplification of a region that contains a regulatory region. |
Regulatory Region Variation | The variant occurs in a regulatory region. |
Consequence | Description |
Gain of Function Variant | The variant results in gain of function. |
Loss of Function Variant | The variant results in loss of function. |
Consequence | Description |
Transcript Variant | The variant changes the structure of the transcript. |
Intron Variant | The variant is completely within the intron region of the gene. |
Exon Variant | The variant is completely within the exon region of the gene. |
Transcript Ablation | A deletion of the region that contains a transcript feature. |
Transcript Amplification | An amplification of a region that contains a transcript. |
Feature Elongation | The variant causes the extension of a genomic feature. |
Feature Truncation | The variant causes the reduction of a genomic feature. |
5-Prime Duplicated Transcript | A partially duplicated transcript in which the 5' end of the transcript is duplicated. |
3-Prime Duplicated Transcript | A partially duplicated transcript in which the 3' end of the transcript is duplicated. |
Consequence | Description |
Unidirectional Gene Fusion | A fusion of two genes on the same strand. |
Bidirectional Gene Fusion | A fusion of two genes on the opposite strand. |
Gene Fusion | A fusion of two genes with ambiguous or unknown strand. |
Consequence | Description |
Gain of Function Variant | The variant results in gain of function. |
Loss of Function Variant | The variant results in loss of function. |
Consequence | Description |
Transcript Variant | The variant changes the structure of the transcript. |
Intron Variant | The variant is completely within the intron region of the gene. |
Exon Variant | The variant is completely within the exon region of the gene. |
Transcript Ablation | A deletion of a region that contains a transcript feature. |
Transcript Amplification | An amplification of a region that contains a transcript. |
Transcript Truncation | A truncation of a region that contains a transcript. |
Feature Elongation | The variant causes the extension of a genomic feature. |
Feature Truncation | The variant causes the reduction of a genomic feature. |
5-Prime Duplicated Transcript | A partially duplicated transcript in which the 5' end of the transcript is duplicated. |
3-Prime Duplicated Transcript | A partially duplicated transcript in which the 3' end of the transcript is duplicated. |
Loss of Heterozygosity | The variant results in loss of heterozygosity of the transcript. |
Type | Description |
Copy Number Increase | The copy number is increased relative to the reference sequence. |
Copy Number Decrease | The copy number is decreased relative to the reference sequence. |
Copy Number Change | The copy number is increased or decreased. |
Intron | The variant is completely within the intron region of the gene. |
Exon | The variant is completely within the exon region of the gene. |
Consequence | Description |
Gain of Function Variant | The variant results in gain of function. |
Loss of Function Variant | The variant results in loss of function. |
Consequence | Description |
Exon Loss Consequence | A loss of one or more exons in a gene. |
Consequence | Description |
Gain of Function Variant | The variant results in gain of function. |
Loss of Function Variant | The variant results in loss of function. |
Consequence | Description |
Unidirectional Gene Fusion | A fusion of two genes on the same strand. |
Transcript Variant | The variant changes the structure transcript. |
Evidence Classification | Haploinsufficiency and TriplosensitivityScore | Suggested Classification |
Sufficient Evidence | 3 | Pathogenic |
Emerging Evidence | 2 | Likely Pathogenic |
Little Evidence | 1 | VUS |
No Evidence | 0 | VUS |
Sensitivity Unlikely | 40: Dosage Sensitivity Unlikely | Likely Benign/Benign |
Autosomal Recessive Phenotype | 30: Autosomal Recessive | Not applicable |
This section provides details on the variant’s presence in different datasets.
Displays the number of samples with the variant in the given workgroup presented per disease. To be accounted for, the variant:
Need to be present in any uploaded VCF or variant file
Need to have a flag PASS in the VCF variant filters
Doesn’t need to be interpreted or included in the report
Can have any variant origin (predicted germline or suspected somatic)
❗ Cases processed prior to version 4.0 of Connected Insights will not appear in the lab frequency.
The section displays:
Number of samples in the Cancer Hotspots database with the variant for the selected transcript
Highest number of samples in the Cancer Hotspots database for the variant across transcripts
The section displays:
Genomic Mutation ID in the COSMIC database
Number of samples with the variant in the COSMIC database displayed per cancer site, for example, breast
Number of samples with the variant in the COSMIC database displayed per histology, for example, carcinoma
This section presents a visualization of the variant in the genome with supporting annotations and surrounding variants.
Reference — Reference genome base pair proportions when zoomed out. Base pair letters and amino acids for a given reading frame when zoomed in.
Genes — RefSeq gene track. Blue indicates the - strand and red indicates the + strand. Click a gene to show the reading frame of the selected transcript for the variant (amino acid and position).
Protein Domains — Displays protein domains from UniProt. Blue indicates the - strand and red indicates the + strand.
Small variants — Small variants shown with the reference allele on top and the two alt alleles below.
Structural variants — Structural variants with VCF filter PASS by chromosomal position. The legend to the right of the genome view identifies the events (translocation, inversion, deletion, insertion, and tandem duplication). Translocations begin at the karyogram at the top of the track and connect to chromosomes identified at the bottom of the track.
Coverage and copy number variants — The depth of coverage by chromosomal position. Data points are color-coded by presence of copy number variant calls. The legend identifies the events (gain, gain LOH, neutral LOH, loss, and no call). Hovering over a region will highlight the copy number variant call and clicking provides variant details.
B-allele ratio — The minor allele frequency by chromosomal position.
Track availability depends on the VCFs provided by the secondary analysis pipeline.
For example,
If there's no structural variant VCF provided, then the structural variant track will not be available.
If there's no absolute copy number provided in the VCF, then the copy number variant track will not be available.
To pan, use the pan controls at the top of the section, or click and drag one of the tracks left or right.
To zoom, use the zoom controls at the top of the section, or hold ctrl and scroll with your mouse or trackpad.
Lists the allele count, allele number, number of homozygotes, and allele frequency for each population from gnomAD for small variants and 1000 Genomes for copy number variants and structural variants. This section is only available for variants.
Connected Insights applies two levels of filtering. The first level is the condition group, which filters data by general information about the variants and is applied to all variants in the view. The second level includes other condition groups with more specific filtering criteria that are applied independently from other condition groups of the second-level filters.
❗ If you are building a filter that covers multiple variant categories, make sure that second level filters cover each of the variant categories that you intend to return with the filter. Including a variant category in the first level filter (eg, copy number variants) but omitting it in second-level filters (even if without filtering conditions) excludes this variant category from the filtering results. For example, filtering logic (Small Variants, CNVs, SVs) AND((Small Variants) OR (CNVs)) excludes SVs from the filtering results. Refer to the following filter examples for more details.
Use the Exclude selector for a given filter to exclude matching variants. The default filter behavior is to include variants.
The first-level condition group:
Does not specify any conditions for genes, thereby including into the filtering results variants from all genes.
Includes into the filtering results all variant categories that Connected Insights supports (for example, small variants SVs, CNVs, RNAsplice variants, and RNA fusions variants).
Sets a condition to include only variants that have PASS in the VCF variant filters, thus excluding all variants that do not have a PASSvalue.
The first-level condition group is connected to the second-level condition groups via operator AND.
The first of the second-level condition group specifies inclusion criteria for small variants to be returned in the filtering results. The condition group sets criteria to capture rare small variants with specific consequences that are of interest:
Variant category is set to Small Variant
Population frequency is specified as equal or less than 0.05 in five population groups in gnomAD
The Consequences filter lists categories of interest: Start Loss, Stop Gained, Stop Loss, and others
The small variants condition group is connected to other second-level condition groups via the operator OR.
The third second-level condition group provides inclusion criteria for RNA Splice Variants. Only PASS-ing (per first-level condition group) RNA Splice Variants with consequence Exon Loss Variant are included in the filtering results.
The next second-level condition group provides inclusion criteria for RNA Fusion Variants. This filtering logic only includes PASS-ing (per first level condition group) Unidirectional Gene Fusions in the filtering results.
The last second-level condition group lists structural variants and copy number variants as variant categories but does not provide any filtering condition. In the current version of Connected Insights, such condition group is required to include structural variants and copy number variants in the filtering results even though they are already specified in the first-level filter.
Column Header | Description |
Interpret | Selecting Interpret allows you to open a Biomarker Details page for that variant to review additional information and perform variant interpretation. After an assertion for this variant has been created for this case, this button lists the highest actionability category for this variant in this case. |
Flag | Allows you to add to the variant a flag with a custom label and color. These flags can be configured in Test Components and can help facilitate variant review. The flags can be used for variant filtering. More than one flag can be added per variant. |
IGV | Selecting IGV opens the Integrative Genomics Viewer (IGV) that can be used to view the sequenced reads at the variant position. |
My Knowledge Base (sortable) | This label indicates the following information: Highest biological classification across all diseases Highest actionability classification across the following: • Diagnostic classifications for all diseases • Prognostic classifications for case and ancestor diseases • Therapeutic classifications for case and ancestor diseases When sorting by this column, variants are ordered by highest classification between biological classification and actionability. If updated assertions for the case disease have been detected, a notification displays in the case header. You can choose to refresh this column with the latest content. |
Other Knowledge Bases (sortable) | This label indicates the following information based on UMLS-DO and UMLS-OncoTree disease mapping: Highest OncoKB biological classification across all diseases Highest OncoKB actionability classification across the following: • Diagnostic classifications for all diseases • Prognostic classifications for case and ancestor diseases • Therapeutic classifications for case and ancestor diseases Highest JAX-CKB actionability classification across the following: • Diagnostic classifications for all diseases • Prognostic classifications for case and ancestor diseases • Therapeutic classifications for case and ancestor diseases Highest CIViC actionability classification across the following: • Diagnostic classifications for all diseases • Prognostic classifications for case and ancestor diseases • Therapeutic classifications for case and ancestor diseases When sorting by this column, variants are ordered first by OncoKB (using highest classification between biological classification and actionability), then by CKB, and finally by CIViC. If updated assertions for the case disease have been detected, a notification displays in the case header. You can choose to refresh this column with the latest content. |
COSMIC (sortable) | The maximum number of samples with the given variant reported in COSMIC. If the variant has a corresponding record in the COSMIC database, and there are multiple COSMIC entries, the sample size associated with the COSMIC entry with the largest sample size is shown. |
Genes | Lists a gene or genes in which the identified variant occurs. Genes, HGVS notations, transcripts, consequence, and other transcript-related variant details are provided for the "default transcript" selected for each variant. |
LOH Overlap | Indicates that the small variant overlaps with a call of LOH. |
CGC (sortable) | The gene role from COSMIC Cancer Gene Census. This information is specific to the gene from the selected transcript. |
Consequences | The impact a variant has on the gene transcripts, such as missense or frameshift. Select More to view a summary of consequences for the variant across all transcripts. |
HGVS | The HGVS coding nomenclature, including p. and c. variant labels. |
Cancer Hotspots (sortable) | The number of samples at the given hotspot in Cancer Hotspots. This information is specific to the Human Genome Variation Society (HGVS) of the selected transcript. Additional samples for other transcripts are indicated in parentheses. |
Pop freq (sortable) | The highest population variant frequency in gnomAD (small variants) or the 1000 Genome Project (structural variants and copy number variants) represented as values from 0 to 1. |
VAF (sortable) | Variant Allele Frequency. The proportion of reads supporting the alternative allele, represented as values from 0 to 1. |
Origin | Indicates whether a variant is Suspected Somatic or Predicted Germline. For tumor-only analyses, when enabled in DRAGEN, the variant origin is determined for small variants based on population frequency databases. For tumor-normal analysis, when enabled in DRAGEN, the variant origin is determined for small variants or structural variants based on the presence or absence of the variant in the normal sample. |
Position (sortable) | Chromosome number and variant position. |
Change | Reference and alternative alleles for small variants (for example, Fold change, absolute copy number, and LOH in case of copy number variants, when available). LOH is determined by a minor copy number (MCN) of 0 for copy number variants with an absolute copy number (CN)greater than 0. |
Quality (sortable) | The quality score reported by the secondary analysis pipeline. |
ClinVar (sortable) | Interpretation categories of VCV entries (aggregate variant records) and RCV entries (aggregate variant-disease records) from ClinVar database. • Pathogenic (P) • Likely pathogenic (LP) • Unknown significance (VUS) • Likely benign (LB) • Benign (B) |
Category (sortable) | Variant category (small variant, structural variant, copy number variant, RNA splice variant, orRNA fusion variant). |
Transcript | Transcript identifier from RefSeq or Ensembl databases. |
OMIM (sortable) | The mode of inheritance reported in OMIM. Highlighted values correspond to the gene of the selected transcript. |
Cytoband (Sortable) | The cytoband location. |
Variant Type | Variant type (SNV, insertion, deletion, and others). |
Exons | Exon or range of exons affected by the variant followed by the total number of exons. |
VCF Filters (sortable) | Value provided for the variant in the FILTER column of the VCF file. Refer to the variant call documentation to confirm possible values and recommended thresholds. |
Length (bp) (sortable) | The length of the variant in bp. |
pLI (sortable) |
SpliceAI (sortable) |
PrimateAI (sortable) |
PrimateAI-3D (sortable) |
PhyloP Score |
Allele Count (sortable) | Alternative allele counts in the gnomAD database. |
Homozygote Count (sortable) | Number of individuals homozygous for alternate allele in the gnomAD database. |
Hemizygote Count (sortable) | Number of individuals hemizygous for alternate allele in the gnomAD database. |
Allele Depth | Number of reads supporting the variant call. |
Total Depth | Number of reads aligned to the position of the variant call. |
Split Reads | Number of reads supporting the variant call spanning the breakpoint. |
Paired Reads | Number of reads supporting the variant call with paired ends supporting the breakpoint. |
Supporting Reads | Number of reads in total supporting the breakpoint. |
Field Name | Description |
Column | Description |
Update Date | The last date that the assertion was updated. |
Source | Knowledge base origin of the clinical trial. |
Status | Indicates the TMB, MSI, or GIS status for the clinical trial. This column is available for TMB, MSI,and GIS. |
HRD | Indicates whether a clinical trial is associated with HRD positive or negative. This column is available for GIS and variants, when the selected transcript is for BRCA1/2. |
Biomarker | Indicates how the assertion is related to the variant (for example, specific amino acid change or specific exon change). |
Title | Title of the clinical trial. |
Phase | Phase of the clinical trial. |
Location | Location of the clinical trial. |
Disease | Disease for the clinical trial. |
Actions |
Connected Insights allows users to create variant interpretation records (assertions). Created assertions are stored in a private database, called My Knowledge Base.
Create Assertions:
Create assertions from scratch, by editing external knowledge base assertions, or by batch-uploading existing assertions.
Create four types of assertions: biological, actionability, clinical trials, and gene descriptions
Collaboration and Management:
Store assertions in a private database, My Knowledge Base.
Collaborate on interpretation with assigned roles.
Manage assertions (view, filter, edit, approve, archive) within or outside specific cases.
Refer to Manage Assertions for more details.
Reporting:
Include variant assertions in reports individually.
Include variant assertions in reports through automation. Refer to Report Automation for more details.
Highlight variants as hereditary risk findings. Refer to Report a Variant as Hereditary Risk Finding
For clinical trials and gene descriptions, refer to Create Clinical Trials or Create Gene Descriptions for more details.
From scratch:
Navigate to the Biomarker Details page.
Click Create New Assertion in the top-right corner or under the list of reported assertions.
In the Classification tab, add information to the fields described below.
From an external knowledge base:
Navigate to the Biomarker Details page.
Find an assertion from an external knowledge base (e.g., CKB).
Select the specific assertion and choose Copy to new assertion from the menu next to "Report".
Add and edit information in the fields described below.
By batch upload existing assertions:
Refer to Assertion Upload for more details.
The Level field describes the genomic change for the assertion. It indicates whether the assertion is related to a specific variant, a group of variants, genomic region, and other factors.
The Consequences field further indicates the applicability of the assertion.
For example, if you are creating an assertion for an EGFR exon 19 deletion, regardless of the specific nucleotide change, the assertion can be specified as follows:
Level: Exon
Consequence: Inframe deletion
The following consequences are available:
Gain of function variant
Loss of function variant
Transcript consequences
When assertions are matched to variants, the consequences field is matched using an OR logic.
For example, if an assertion has the stop gained, start lost, and frame shift variant consequences, it can be matched to any variant that has at least one of those consequences.
For biological assertions, if the gain of function variant or loss of function variant is specified, this variant is annotated with these consequences in future cases or if you refresh the case assertions.
If a variant is annotated with these consequences, then the relevant assertions are shown (e.g., evidence for activating mutations).
The Status field indicates the status of TMB, MSI, and GIS that the assertion is applicable to.
The following categories are available:
TMB-High
TMB-Low
MSI-High
MS-Stable
GIS-High
GIS-Low
The HRD field indicates if the assertion is related to HRD for GIS and BRCA1 and BRCA2 variants.
The following categories are available:
Undetermined
Positive
Negative
The Type field indicates whether the assertion describes the variant's biological classification or actionability.
The following selections are available:
Biological
Therapeutic
Prognostic
Diagnostic
The Direction field indicates the overall observation for the evidence the assertion is describing.
The following selections are available for therapeutic assertions:
Responsive
Non-Responsive
Contraindicated
The following selections are available for prognostic assertions:
Favorable
Unfavorable
The Therapy field indicates the therapy context for the assertion. This field is only available for therapeutic assertions.
To add a drug, search for drug names using RxNorm terms.
For assertions with drug combinations, select more than one drug in the same assertion. For assertions with a single drug, select one drug per assertion.
The Disease field indicates the disease context for the assertion.
Diseases can be searched using SNOMEDCT terms.
For Biological assertions, the default selection is neoplastic disease.
For all other assertions, the default is the disease of the case.
The Classification field is used to specify the biological or actionability classification.
For biological assertions:
Available selections are Oncogenic, Likely Oncogenic, Pathogenic, Likely Pathogenic, VUS, Likely Benign, and Benign.
For actionability assertions:
The default selections are based on Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.
To set up your own classification categories, following the guidance in Custom Actionability Classification
The Summary field is a free text field for an assertion summary. The summaries are displayed in the report.
The Notes field is a free text field for internal notes related to the assertion. The notes are not displayed in the report.
The Approval Status field indicates the assertion approval status. See Manage Assertions for more details.
Reports can indicate hereditary risk findings to list variants suspected or confirmed to be of germline origin that could be associated with hereditary cancer risk. To indicate a variant is a hereditary risk finding in the report:
Navigate to the Biomarker Details page.
Create or report at least one assertion.
Select the Also report as a hereditary risk finding? checkbox that appears in the top-right corner.
The Oncogenicity Prediction feature estimates oncogenic potential of variants based on Standards for the classification of somatic variants in cancer (Horak et al., Genet Med. 2022). The standards include 17 criteria and allow to classify variants into 5 categories: Oncogenic, Likely Oncogenic, Variant of Unknown Significance (VUS), Likely Benign, and Benign. Connected Insights scores variants (only PASS small variants are currently supported) for 16 criteria (with exception of OP2) based on the implementation details provided below.
❗ Use predictions as a starting point for interpretation. Exercise judgement to determine if a greater or fewer number of criteria apply.
Estimated variant oncogenicity can be found:
In the column “Oncogenicity Prediction” in the Variants tab available for sorting
In the section “Oncogenicity Prediction” in the Biomarker page available for manual review and further interpretation
To view the evidence behind the estimated oncogenicity category and complete variant classification, follow the steps below:
Navigate to the "Oncogenicity Prediction" section in the Biomarker page
Review estimated oncogenicity category, score, and met criteria (displayed with filled checkboxes, see OS2, OM1, OM2, OP3, and OP4 on the figure below)
Review evidence for each criterion by clicking on it and displaying an evidence map. You can move objects on the map to facilitate review.
Select Report to edit and complete variant classification following Interpret a Variant. Information about met oncogenicity criteria is used to pre-populate variant summary.
OVS1: “Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a bona fide tumor suppressor gene.”
For this criterion, we are checking the fulfillment of the following conditions:
Variant is a “null variant”. We assess null variants as variants with consequences stop_gained, start_lost, frameshift_variant, splice_acceptor_variant, or splice_donor_variant as well as variants with a high splicing prediction (SpliceAI score > 0.8) regardless of their consequences
Variant is not in the last intron or exon
Variant is in a tumor suppressor gene, according to Cancer Genome Census, JAX-CKB, OncoKB or MyKB
OS1: “Same amino acid change as a previously established oncogenic variant regardless of nucleotide change. Example: Val→Leu caused by either G>C or G>T in the same codon.”
For this criterion, we are checking the fulfillment of the following conditions:
Variant's consequences are not splice_donor_variant or splice_acceptor_variant
Variant’s splicing prediction is not high (SpliceAI score <= 0.8)
There is a previously established pathogenic / oncogenic or likely pathogenic / oncogenic variant with the same amino acid change but different nucleotide change in ClinVar (2-4 stars) or MyKB
OS2: “Well-established in vitro or in vivo functional studies supportive of an oncogenic effect of the variant.”
For this criterion, we are checking the fulfillment of the following conditions:
A variant with the same amino acid change is a gain-, loss-, or switch-of-function variant in MyKB, OncoKB, or JAX-CKB, is interpreted as pathogenic / oncogenic or likely pathogenic / oncogenic in MyKB, OncoKB, JAX-CKB, or ClinVar (2-4 stars), and OS1 is not applicable OR
A variant with the same nucleotide change is a gain-, loss-, or switch-of-function variant in MyKB, OncoKB, or JAX-CKB, is interpreted as pathogenic / oncogenic or likely pathogenic / oncogenic in ClinVar (2-4 stars), and OS1 is applicable
In this implementation, “Well-established in vitro or in vivo functional studies” is inferred based on knowledge bases having records of gain-, loss-, or switch-of-function, usually established based on functional studies. “... supportive of an oncogenic effect of the variant” is established based on the evidence of oncogenicity in knowledge sources.
OS3: “Located in one of the hotspots in cancerhotspots.org with at least 50 samples with a somatic variant at the same amino acid position, and the same amino acid change count in cancerhotspots.org in at least 10 samples.”
For this criterion, we are checking the fulfillment of the following conditions:
There are at least 50 samples with somatic variants at the same amino acid position in cancerhotspots.org, there are at least 10 samples with variants with the same amino acid change in cancerhotspots.org and OS1 is not applicable OR
There are at least 50 samples with somatic variants at the same amino acid position in COSMIC, there are less than 10 samples with variants with the same amino acid change in cancerhotspots.org and OS1 is not applicable OR
There are at least 50 samples with somatic variants at the same nucleotide position in cancerhotspots.org, there are at least 10 samples with a variant with the same nucleotide change in cancerhotspots.org and OS1 is applicable OR
There are at least 50 samples with somatic variants at the same nucleotide position in COSMIC, there are less than 10 samples with a variant with the same nucleotide change in cancerhotspots.org and OS1 is applicable
OM1: “Located in a critical and well-established part of a functional domain (e.g., active site of an enzyme).”
For this criterion, we are checking the fulfillment of the following conditions:
The variant is located in a region of a protein domain where pathogenic variants occur. The regions in each gene are defined by taking all protein domains from UniProt, mapping all pathogenic and likely pathogenic variants in ClinVar to each domain and defining the regions by using the positions of the first and last pathogenic and likely pathogenic variants from ClinVar and adding 2 bp padding on each side.
OS1 and OS3 are not applicable
OM2: “Protein length changes as a result of in-frame deletions / insertions in a known oncogene, or tumor suppressor gene or stop-loss variants in a known tumor suppressor gene.”
For this criterion, we are checking the fulfillment of the following conditions:
Variant’s consequence is inframe_deletion or inframe_insertion and it is located in an oncogene or a tumor suppressor gene (based on Cancer Genome Census, JAX-CKB, OncoKB or MyKB) or variant’s consequence is stop-lost and it is located in a tumor suppressor gene per the same sources
OVS1 is not applicable
OM3: “Located in one of the hotspots in cancerhotspots.org with less than 50 samples with a somatic variant at the same amino acid position, and the same amino acid change count in cancerhotspots.org is at least 10.”
For this criterion, we are checking the fulfillment of the following conditions:
There are less than 50 samples with somatic variants at the same amino acid position in cancerhotspots.org, there are at least 10 samples with variants with the same amino acid change in cancerhotspots.org , and OM1 and OM4 are not applicable OR
There are 10 - 49 samples with somatic variants at the same amino acid position and change in COSMIC, there are less than 10 samples with variants with the same amino acid change in cancerhotspots.org , and OM1 and OM4 are not applicable
OM4: “Missense variant at an amino acid residue where a different missense variant determined to be oncogenic (using this standard) has been documented. Amino acid difference from reference amino acid should be greater or at least approximately the same as for missense change determined to be oncogenic.”
For this criterion, we are checking the fulfillment of the following conditions:
There is a missense variant at the same amino acid position with a different amino acid change interpreted as pathogenic / oncogenic or likely pathogenic / oncogenic in ClinVar (2-4 stars), OncoKB or MyKB
OS1, OS3 and OM1 are not applicable
OP1: “All utilized lines of computational evidence support an oncogenic effect of a variant (conservation / evolutionary, splicing impact, etc.).”
For this criterion, we are checking the fulfillment of the following conditions:
Variant’s effect predicted to be damaging (REVEL > 0.75 and PrimateAI-3D score percentile > 0.8) or variant’s splicing prediction is high (SpliceAI score > 0.8)
OP2: “Somatic variant in a gene in a malignancy with a single genetic etiology.”
This criterion is not yet implemented.
OP3: “Located in one of the hotspots in cancerhotspots.org and the particular amino acid change count in cancerhotspots.org is below 10.”
For this criterion, we are checking the fulfillment of the following conditions:
There is at least 1 sample with a somatic variant at the same amino acid position in cancerhotspots.org or COSMIC
There are less than 10 samples with variants with the same amino acid change in both, cancerhotspots.org and COSMIC
OP4: “Absent from controls (or at an extremely low frequency) in Genome Aggregation Database (gnomAD).”
For this criterion, we are checking the fulfillment of the following conditions:
Variant’s allele count in the global population (gnomAD) is less than 10 if the variant is not in TP53, KRAS, or PTEN
Variant is absent in the global population (gnomAD) if the variant is in TP53 or KRAS
Variant’s frequency in the global population is less than 0.001% (gnomAD) if the variant is in PTEN
SBVS1: “Minor allele frequency is >5% in Genome Aggregation Database (gnomAD) in any of 5 general continental populations: African, East Asian, European (Non-Finnish), Latino, and South Asian.”
For this criterion, we are checking the fulfillment of the following conditions:
Variant’s frequency in any one population is over 5% (gnomAD) if the variant is not in TP53, KRAS or PTEN
Variant’s frequency in the global population is equal or over 0.1% (gnomAD) and allele count in the global population is equal or over 5 (gnomAD) if the variant is in TP53
Variant’s frequency in the global population is equal or over 0.05% (gnomAD) if the variant is in KRAS
Variant’s frequency in the global population is equal or over 1% (gnomAD) and allele count in the global population is equal or over 5 (gnomAD) if the variant is in PTEN
SBS1: “Minor allele frequency is >1% in Genome Aggregation Database (gnomAD) in any of 5 general continental populations: African, East Asian, European (Non-Finnish), Latino, and South Asian.”
For this criterion, we are checking the fulfillment of the following conditions:
Variant’s frequency in any one population is over 1% (gnomAD) if the variant is not in TP53, KRAS or PTEN
Variant’s frequency in the global population is over 0.03% (gnomAD) and allele count in the global population is equal or over 5 (gnomAD) if the variant is in TP53
Variant’s frequency in the global population is equal or over 0.025% (gnomAD) if the variant is in KRAS
Variant’s frequency in the global population is equal or over 0.1% (gnomAD) and allele count in the global population is equal or over 5 (gnomAD) if the variant is in PTEN
SBS2: “Well-established in vitro or in vivo functional studies show no oncogenic effects.”
For this criterion, we are checking the fulfillment of the following conditions:
Variant is interpreted as benign or likely benign in ClinVar (2-4 stars), OncoKB or MyKB
SBP1: “All used lines of computational evidence suggest no effect of a variant (conservation / evolutionary, splicing effect, etc.).”
For this criterion, we are checking the fulfillment of the following conditions:
Variant’s effect predicted to be neutral (REVEL is equal or less than 0.75 and PrimateAI-3D score percentile is equal or less than 0.8)
Variant’s splicing prediction is low or unknown (SpliceAI score is equal or less than 0.2 or unknown)
SBP2: “A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved.”
For this criterion, we are checking the fulfillment of the following conditions:
Variant has a consequence synonymous_variant
Variant’s conservation prediction score is not high (PhyloP < 0.1)
Variant’s splicing prediction is low or unknown (SpliceAI score <= 0.2)
The Biological Classification section of the Biomarker Details page summarizes all biological assertions previously created for the variant across all sources (e.g., My Knowledge Base or JAX-CKB). If you have existing knowledge to upload to the system, refer to Upload Assertions.
You can also filter by other diseases and by summary.
Filter changes are saved and applied across variants within a case and can be reset if needed.
Connected Insights provides the Memorial Sloan Kettering OncoKB. For more information, refer to the OncoKB website.
The following from OncoKB are not supported:
Non-compliant HGVS
Unspecified positions: Epigenetic Silencing, ARv567es, AR-V7, DNMT3B7, vIII, vII, vV, TGFBR1*6A, Overexpression, Wildtype, Promoter Hypermethylation, Hypermethylation, Kinase Domain Duplication, Internal Tandem Duplication, Partial Tandem Duplication
Connected Insights provides the Jackson Clinical Knowledge Base (JAX-CKB). For more information, refer to the Jackson CKB website.
The following from JAX-CKB are not supported:
Complex molecular profiles (for example, co-occuring biomarker assertions)
Emerging and risk factor evidence types
Class #, over exp, dec exp, hypermethylation, hypomethylation, dup exonX, dup exonX-X, LOH, loss, negative (except for HRD andMSI), positive (except for HRD), and wild type variants.
A single table in the biomarker details provides a list of all the diagnostic assertions from all included sources that have content about the biomarker (e.g., My Knowledge Base).
You can filter by other diseases or by summary. When filtering by summary for guideline evidence, specify the website (for example, ESMO.org or NCCN.org).
Filter changes are saved and applied across variants within a case and can be reset if needed.
A single table in the biomarker details provides a list of all the therapeutic and prognostic assertions from all included sources that have content about the biomarker (e.g., My Knowledge Base).
By default, the assertions are filtered by the case and ancestor diseases. Ancestor diseases are determined using SNOMEDCT. These diseases can be viewed at the SNOMED CT Browser website, with the following exceptions:
Descendents of neoplastic disease do not include ancestors beyond neoplastic disease.
Non-small cell lung cancer has been added as an ancestor of adenocarcinoma of lung.
You can filter by other diseases, by summary, or by approval. When filtering by summary for guideline evidence, specify the website (for example, ESMO.org or NCCN.org).
Filter changes are saved and applied across variants within a case and can be reset if needed.
Connected Insights provides the Memorial Sloan Kettering OncoKB. For more information, refer to the OncoKB website.
The following from OncoKB are not supported:
Non-compliant HGVS
Unspecified positions: Epigenetic Silencing, ARv567es, AR-V7, DNMT3B7, vIII, vII, vV, TGFBR1*6A, Overexpression, Wildtype, Promoter Hypermethylation, Hypermethylation, Kinase Domain Duplication, Internal Tandem Duplication, Partial Tandem Duplication
Connected Insights provides the Jackson Clinical Knowledge Base (JAX-CKB). For more information, refer to the Jackson CKB website.
The following from JAX-CKB are not supported:
Complex molecular profiles (for example, co-occuring biomarker assertions)
Emerging and risk factor evidence types
Class #, over exp, dec exp, hypermethylation, hypomethylation, dup exonX, dup exonX-X, LOH, loss, negative (except for HRD andMSI), positive (except for HRD), and wild type variants.
Connected Insights also provides the Clinical Interpretation of Variants in Cancer (CIViC) knowledge base. For more information, refer to the CIViC website.
The following from CIViC are not supported:
Assertions
Functional and oncogenic evidence types
Splice Site (c.3028G>A), Boolean-like evidence (for example, (V600E or V600K) and Amplification), Underexpression, Overexpression, Expression, Decreased Peri-therapeutic Expression, Cytoplasmic Expression, Loss, Biallelic Inactivation, Alu Insertion, Alternative Transcript, RSID, Homozygosity, Copy-neutral Loss of Heterozygosity, Cytoplasmic Mislocation, Deleterious Mutation, Double Ph, Wildtype, Domain, Exon-specific fusions
This section is only available for variants that overlap a transcript.
A list of all genes overlapping the variant are provided. Select one to view the details below.
Column | Description |
---|---|
Memorial Sloan Kettering OncoKB
Connected Insights provides the Memorial Sloan Kettering OncoKB. For more information, refer to the OncoKB website.
Jackson Clinical Knowledge Base (JAX-CKB)
Connected Insights provides the Jackson Clinical Knowledge Base (JAX-CKB). For more information, refer to the Jackson CKB website.
Clinical Interpretation of Variants in Cancer (CIViC)
Connected Insights also provides the Clinical Interpretation of Variants in Cancer (CIViC) knowledge base. For more information, refer to the CIViC website.
The associated phenotypes in ClinGen and OMIM databases and links to open the entries in the databases in a new browser tab.
The following external links are included in this section:
PubMed
MGI
DECIPHER
GeneReviews
Monarch
ZFIN
STRING
The score applies to the selected transcript. If the score is different across transcripts, the highest score is displayed in parentheses after the score for the selected transcript. For more information, refer to .
The score can be interpreted as the probability of the variant being splice-altering. For more information, refer to .
A deep residual neural network for classifying the pathogenicity of missense mutations. The score applies to the selected transcript. If the score is different across transcripts, the highest score is displayed in parentheses after the score for the selected transcript. For more information, refer to .
A three-dimensional (3D) convolutional neural network for classifying the pathogenicity of missense mutations. The score applies to the selected transcript. If the score is different across transcripts, the highest score is displayed in parentheses after the score for the selected transcript. For more information, refer to .
This score measure evolutionary conservation at individual alignment sites. For more information, refer to .
This column contains the following available actions: • Select the hyperlink to display the full listing about the trial in a new browser tab. • Add to report • Archive, if the assertion is in My Knowledge Base • Copy to New Assertion, if the assertion is not in My Knowledge Base • View past cases To edit an assertion, add it to the report before editing. For more information, refer to .
Level | Description |
---|---|
Field Name
Description
VCF Column
Required Value
Variant Type
Type of the variant: SNV, insertion, deletion, MNV
Chromosome
The reference sequence name. Values are #, or chr#, where # is 1 of the following: •The chromosome number, as in 1–22. •The name, as in X or Y; M or MT for mitochondrial.
Start
Start position.
Stop
Stop position.
Variant ID
Variant ID from Nirvana, based on the Broad variant ID scheme.
Ref Allele
The reference allele.
Alt Allele
The alternate allele.
Genes
Name of the gene if applicable. A comma-delimited list is used for multiple genes.
Exons
Exon number(s) and the total exons for the active transcript, as applicable. A comma-delimited list is used for multiple exons.
Cytogenetic Band
Cytoband of variant.
All Consequences
Sequence Ontology consequences to describe how each variant impacts a given transcript.
Field Name
Description
Database
Database Description
IGV
Integrative Genomics Viewer (IGV) is an open-source genome browser and visualization tool used to observe biologically interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
LOVD
The Leiden Open Variation Database (LOVD) is an open-source database focused on the combination between a gene and a genetic (heritable) disease.
UCSC Browser
An interactive database offering access to genome sequence data from various vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
Ensembl
A bioinformatics project organizing biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them..
gnomAD
A database that aggregates and harmonizes both exome and genome sequencing data from a wide variety of large-scale sequencing projects.
COSMIC
An online database of somatically acquired mutations found in human cancer. This link opens COSMIC in a new browser tab.
Google Scholar
Google Scholar provides a way to broadly search for scholarly literature. Search across many disciplines and sources, including: • Articles • Theses • Books • Abstracts This information comes from academic publishers, professional societies, online repositories, universities, and other web sites.
PubMed
PubMed allows you to search for literature for the variant.
LitVar
LitVar allows you to search for literature for the variant. This is available for any variant with an RSID.
Mastermind
Mastermind allows you to search for literature for the variant. This is available for any variant with an hgvsg annotation.
Nucleotide
Specific assertion for genome build, chromosome, position, reference allele, and alternate allele. Available for small variants with transcript annotation.
Amino Acid
Specific assertion for amino acid. Available for small variants with HGVSP annotation.
Codon
Specific assertion for codon. Available for small variants with HGVSP and missense consequence annotation.
Exon
Specific assertion for exon. Available for small variants and copy number variants with exon annotation.
Gene
Specific assertion for gene. Available for small variants with gene annotation.
Annotation Overlap
Specific assertion for genome build and genomic range. Available for large variants and RNA splice variants.
Partial Fusion
Specific assertion for at least one gene. Available for RNA fusion variants.
Exact Fusion
Specific assertion for gene, fusion gene, and fusion directionality. Available for structural variants and RNA fusion variants with a fusion gene.
Field Name
Description
Column
Description
Directional Arrows
Opens to view the assertion summary.
Update Date
The last date that the assertion was updated.
Biomarker
Indicates how the assertion is related to the variant (for example, specific amino acid change or specific exon change).
HRD
Indicates whether an assertion is associated with HRD positive or negative. This column is available for GIS and variants when the selected transcript is for BRCA1/2.
Classification
This column displays the classification as indicated by the knowledge base.
Type
The assertion type (for example, biological). For more information, refer to Interpret a Variant.
Disease
The disease associated with the classification.
Actions
This column contains the following available actions: • Add to report • Archive, if the assertion is in My Knowledge Base • Copy to New Assertion, if the assertion is not in My Knowledge Base • View past cases To edit an assertion, add it to the report before editing. For more information, refer to Manage Assertions.
Field Name
Description
Column
Description
Published Date
The date that the assertion was updated.
Source
Knowledge base origin of the assertion.
Biomarker
Indicates whether an assertion is the nucleotide, annotation overlap, partial fusion, amino acid,codon, exon, or gene level. This column is only available for variants.
Status
Indicates the TMB, MSI, or GIS status for the assertion. This column is available for TMB, MSI, and GIS.
HRD
Indicates whether an assertion is associated with HRD positive or negative. This column is available for GIS and variants when the selected transcript is for BRCA1/2.
Classification
This column displays the classification (for example, Tier 1A), as indicated by the knowledge base.
Type
Therapeutic, Diagnostic, or Prognostic as indicated by the knowledge base.
Direction
• For therapeutic; responsive, nonresponsive, etc., as indicated by the knowledge base. • For prognostic; favorable, unfavorable, etc., as indicated by the knowledge base.
Therapy
Therapy for the assertion.
Disease
Disease for the assertion.
Approval
Authorities that have approved the therapy for the biomarker and disease. • CKB provides FDA, EMA, ANVISA, PDMA, and TGA approvals. • OncoKB level 1 assertions are annotated with FDA.
Actions
This column contains the following available actions: • Add to report • Archive, if the assertion is in My Knowledge Base • Copy to New Assertion, if the assertion is not in My Knowledge Base • View past cases To edit an assertion, add it to the report before editing. For more information, refer to Manage Assertions.
Update Date
The last date that the assertion was updated.
Source
Knowledge base origin of the gene description.
Role
The specified gene role.
Summary
Gene description.
Actions
This column contains the following available actions: • Add to report • Archive, if the assertion is in My Knowledge Base • Copy to New Assertion, if the assertion is not in My Knowledge Base • View past cases To edit an assertion, add it to the report before editing. For more information, refer to Manage Assertions.
Field Name
Description
Tool
Description
REVEL
The Rare Exome Variant Ensemble Learner (REVEL) is an ensemble method for predicting the pathogenicity of rare missense variants. Scores range from 0 to 1 and variants with highers cores are predicted to be more likely to be pathogenic.
SIFT
The Sort Intolerant From Tolerant (SIFT) score predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physicochemical similarity between the alternate amino acids. The qualitative prediction for substitutions with a score less than 0.05 are predicted to be deleterious. All other variants are considered tolerated.
PolyPhen-2
Polymorphism Phenotyping-2, or PolyPhen-2, predicts the effect of an amino acid substitution on the structure and function of a protein using the following components: • Sequence homology • Pfam annotations • 3D structures from PDB (where available) • Other databases and tools (for example, DSSP and ncoils) The PolyPhen-2 score represents the probability that a substitution is damaging, so values near1 are predicted to be deleterious, which is the opposite of the SIFT score.
PrimateAI
PrimateAI is a deep residual neural network for classifying the pathogenicity of missense mutations. For more information, refer to Acronyms and Terms.
PrimateAI-3D
PrimateAI-3D is a three-dimensional (3D) convolutional neural network for classifying the pathogenicity of missense mutations. For more information, refer to Acronyms and Terms.
Nirvana Cross-SpeciesAA Conservation
Nirvana Cross-Species AA Conservation uses amino acid conservation scores that are obtained from multiple alignments of vertebrate exomes to the human ones. The score indicates the frequency with which a particular AA is observed in humans.
PhyloP
PhyloP scores measure evolutionary conservation at individual alignment sites. For more information, refer to Acronyms and Terms.
SpliceAI
SpliceAI is the delta score of a variant that can also be interpreted as the probability of the variant being splice-altering. For more information, refer to Acronyms and Terms.
gnomAD
gnomAD consists of the following items: • Constraint metrics • LOEUF • misZ • pLi • pNull • pRec • synZ For more information, refer to Acronyms and Terms.
This section provides information on how to create and customize reports using a template.
From the Case List, you may upload case metadata files to update the metadata for existing cases or create new cases if those cases do not already exist. Cases created in this way will be in an Awaiting Molecular Data status until secondary analysis output data is associated to the samples of those cases, see Data Upload Configuration for details on uploading molecular data. For more information on the custom case data format, refer to Custom Case Data Upload.
Upload a case metadata file as follows:
From the Case List, select + New Case.
Select the Import from CSV File option and click the button for Import from CSV File.
[Optional] Download the attached template and input the desired case metadata to upload.
Select a case metadata file to upload (up to five files may be uploaded at one time).
Select Proceed.
From the Case List, select Upload Case Metadata.
Select View Past Uploads from the dropdown.
[Optional] Select Refresh Uploads to refresh the status and details for uploaded files.
[Optional] Download CSVs containing a record of problematic rows for files that were not successfully processed.
Connected Insights supports merging RNA and DNA cases with the same case subject. For instructions on how to change the case subject, refer to Case Details. Merge cases as follows.
Select the applicable case.
Select the Overview tab, and then select Case Details to open the Case Details pane.
Select Related Cases. All cases (including DNA, RNA, and DNA+RNA cases) with the same case subject display.
Select Merge Cases.
Configure the case as follows. a. To merge a DNA case, select Select DNA Case and choose from a drop-down list with applicable DNA cases. b. To merge an RNA case, select Select RNA Case and choose from a drop-down list with applicable RNA cases. c. [Optional] To change the case number, enter a new case ID. d. Select the applicable definition from the Confirm Test Definition drop-down list. This option defaults to the DNA case test definition. e. Select the disease associated with the merged case. This field can be the same or different disease from the one that is in the DNA and RNA cases that are you merging.
Select Confirm.
Make sure that the new case displays under the Case Timeline in the Case Details sidebar. When the merged case is selected, Connected Insights indicates that the case was created from merging the RNA and DNA cases.
The Visualize tab provides different visualizations for structural events and Variant Allele Frequency (VAF) distribution through the following tabs:
Genome View
VAF Distribution
The Genome View tab shows an overview of the following events:
Structural variants — Structural variants with VCF filter PASS by chromosomal position. The legend to the right of the genome view identifies the events (translocation, inversion, deletion, insertion, and tandem duplication). Translocations begin at the karyogram at the top of the track and connect to chromosomes identified at the bottom of the track.
Coverage and copy number variants — The depth of coverage by chromosomal position. Data points are color-coded by presence of copy number variant calls. The legend identifies the events (gain, gain LOH, neutral LOH, loss, and no call). Hovering over a region will highlight the copy number variant call and clicking provides variant details.
B-allele ratio — The minor allele frequency by chromosomal position.
Small variants - Small variants with VCF filter PASS by chromosomal position. Data points can be color-coded by variant type or substitution. Y-axis can display VAF or intermutational distance (requires sufficient zoom).
The Genome View can be shown in the following displays:
Linear plot - Chromosomes are arranged sequentially in a linear manner.
Circos plot - Chromosomes are arranged sequentially in a circular manner with translocations in the center ring.
Track availability depends on the VCFs provided by the secondary analysis pipeline.
For example,
If there's no structural variant VCF provided, then the structural variant track will not be available.
If there's no absolute copy number provided in the VCF, then the copy number variant track will not be available.
Genome View is not available for cases created in Connected Insights v1.0.
Click on a chromosome to zoom into a chromosome.
Or use the Search field at the top of the section to search for a location by specifying one of the following:
Chromosome (for example, chr2)
Range (for example, chr2:0-24219350)
Position (for example, chr2:10000)
After entering search information, press Enter to view the location.
After clicking on a chromosome or searching for a location:
To pan, use the pan controls at the top of the section, or click and drag one of the tracks left or right.
To zoom, use the zoom controls at the top of the section, or hold ctrl and scroll with your mouse or trackpad.
To return to the all chromosomes view, remove any values from the Search field or type all and press Enter.
The VAF Distribution tab provides an overview of the VAF across the SNV and Delins variant types. Hover over the bars on the graph to show the number of variants associated with the VAF. The VAF is calculated as alt/(alt + ref), where alt and ref are the number of reads supporting the non-reference and reference bases. VAF depends on the following characteristics:
Tumor ploidy
Cancer heterogeneity
Copy number variations
You can also select Explain Plot to view this information.
The Variant Type drop-down list above the graph has two selectable options: SNV or Delins. The SNV option shows small variant SNVs with VCF filter PASS. The Delins option shows small variant delins, insertions, and deletions with VCF filter PASS.
Select a variant in the Structural Variants and Copy Number Variants tracks to navigate the variant details. For more information, refer to .
Connected Insights provides users with the flexibility to apply a selection of filter criteria to each variant category supported in the software. The selection of variant categories impacts the set of filtering criteria that can be selected for a given filter group.
The following table summarizes filters available for each variant category:
Variant Category
Small Variants
Structural Variants
Copy Number Variants
RNA Splice Variants
RNA Fusion Variants
COSMIC
+
CGC
+
+
+
+
+
Cancer Hotspots
+
+
+
+
+
Change (Copy Number)
+
Change (Fold Change)
+
ClinVar (VCV, RCV)
+
+
+
+
+
Consequences
+
+
+
+
+
Constraint Metrics(gnomAD)
+
+
+
+
+
Filters
+
+
+
+
+
Flags
+
+
+
+
+
Genes
+
+
+
+
+
Haploinsufficiency(ClinGen)
+
+
+
+
+
Length
+
+
+
+
+
Low Complexity Region(gnomAD)
+
OMIM
+
+
+
+
+
Origin
+
+
+
+
+
Population
+
+
+
Position (Chromosome)
+
+
+
+
+
Position (Genomic Regions)
+
+
+
+
+
PrimateAI-3D
+
LOH Overlap
+
+
+
+
+
Sample Metrics
+
+
+
+
+
Splice AI
+
Triplosensitivity (ClinGen)
+
+
+
+
+
Variant Type
+
+
+
Connected Insights includes the Population filter that filters small variants based on the population allele frequency provided in the gnomAD database or custom annotations (refer to Custom Annotations).
The same Population filter is used to filter CNVs and SVs. For these variant categories, the filter uses the aggregate population allele frequency as calculated by Connected Insights based on the data provided in the 1000 Genomes Project database. The aggregation addresses challenges from significant variability in the calling of CNV and SV boundaries and the need to consider frequency of variants with close boundaries in aggregation. For example, allele frequency of variants 1000–2000 CNV gain and 1005–2000 CNV gain are considered as a sum). Specifically:
We selected alleles with 300 samples or more given the population group in the 1000 Genomes Project.
We aggregated alleles based on their similarity defined by the reciprocal overlap being equal or exceeding 0.75.
We calculated the aggregate frequency as the sum of all allele frequencies of the similar CNVs per given population group.
❗ The population frequency filter is only selectable in a filter group with a single selected variant category, as the population frequencies are tied to specific variant categories. The filter is not available for RNA Splice Variants and RNA Fusion Variants.
❗ The population frequency for copy number variants and structural variants is not displayed for alleles found in fewer than 300 samples per given population group in the 1000 Genomes Project.
The custom pipeline option is designed to make Connected Insights understand the structure of the secondary analysis output files produced by a pipeline that is not yet compatible with the software. This option also requires the creation of a workflow schema file that describes the content and location of the secondary analysis output files. For an example of a how to configure a custom pipeline for TSO 500 Analysis Module v2.2, refer to Custom Pipeline Configuration Example.
In Configuration Settings, select the radio button next to Configure custom pipeline.
If necessary, create a workflow schema file by selecting Download the template file. For more information on setting up the template file, refer to Create a Workflow Schema File
Select Choose File to upload your template file.
For Custom Pipeline Name, enter a name for the pipeline.
For Test Definition, select the applicable definition.
For the Choose a folder to monitor for case metadata (optional) field, enter the path for the folder in the secondary analysis folder created by Data Uploader.
Select Save.
To set up data upload for secondary analysis output data that is not yet compatible with Connected Insights, create a workflow schema file (.yaml format). This file specifies the files in the secondary analysis output data that Connected Insights analyzes. This file is only used when configuring a custom pipeline.
Download a workflow schema file template from Connected Insights as follows.
On the top toolbar, select Configuration.
Select the General tab.
Select Data Upload.
Select From Local Storage.
For Define and Monitor Data Uploads, select Add Path.
For Configuration Settings, select the radio button next to Configure custom pipeline.
Select Download a template file to download the workflow schema template file. If you do not want to create a pipeline, select Cancel. When prompted, select Yes, clear.
Edit the file as needed to reflect the files for upload. Refer to the following topics that pertain to the workflow schema template file sections:
❗ If, Optional is after the file name, then Connected Insights uploads the file if it is available or moves on to the next available file.
After the workflow schema file is edited, create a pipeline. Then, select Configure manually under Configuration Settings.
Select Choose File and upload the edited workflow schema file.
Complete the remaining fields and save the pipeline.
❗ If this pipeline is used for manual uploading, make sure that the pipeline name only consists of numbers, letters, underscores, and dashes. The name cannot include spaces or special characters. This name is used in the --pipeline-name= command listed in On-Demand Data Upload from User Storage (Connected Insights - Cloud Only)
This section of the file can be partially or completely deleted if uploading does not entail any (or all) of the following aspects:
Required
successMarkerFile and failureMarkerFile: Specify a success marker file or failure marker file. When this file is present in the specified location, upload begins or stops, respectively.
Optional
sampleType — If the given analysis output belongs to only DNA or RNA, you can override the samples with the sampleType. If the sample Type is not specified, the system determines it from the analysis output.
This section specifies the sample sheet file path found in the analysis folder, the data header row marker, and column aliases. The following information is used to create cases in Connected Insights:
Required
filePath — Adding a file path to the sample sheet for the cases.
Optional
columnAliases — Specify the column aliases. These aliases must match the sample information column headers. Some aliases are required and others are optional.
sampleId — Appears in the Case ID column of the Cases page.
caseId — Appears in the Case ID column of the Cases page. For DNA-RNA paired samples, both the DNA and RNA sample rows have the same value in the column whose header is aliased to caseId. If the caseId is aliased to column header Pair_ID, a DNA-RNA sample must contain the same value in the Pair_ID column in both the DNA and RNA sample rows in Sample Sheet.
Sample_Type — No alias can be made for Sample_Type. The sample sheet must include a column header titled Sample_Type with all sample rows containing DNA or RNA in this column.
sex — Aliased to the header title of the column containing the sex of each sample.
Disease aliases — Determine the list of Key Genes used for this sample. For more information, refer to Overview Tab. If the disease name or ID is not provided, then the Status column on the Cases page displays Missing Required Data. This message displays until the disease name or ID is added. You can add a disease by uploading disease information as custom case data.You can also open the case in Connected Insights and enter the disease for an individual case.
id — Can be optionally aliased to the header title of the column containing sample disease ID number according to SNOMEDCT. The SNOMEDCT ID can be found by navigating to an existing case and searching for the disease in the CaseDetails or assertion form. The ID can also be found by using the International Edition browser at the SNOMED International SNOMED CT Browser.
name — Can be optionally aliased to the header title of the column containing sample disease name according to SNOMEDCT.If a disease ID is specified, a name is required. If you would not like to specify a name while using a disease ID, enter a null, or any non-exist column for the name field.
dataHeaderRowMarker - Specify the sample sheet data header row marker. The default value is [Data]. This specifies that the next row (one row below) contains the sample information headers and that the rows below that (two rows below and beyond) contain the sample information values for each sample. This should be the sample sheet cell text in the first column (furthest left) one row above the row containing the column headers describing the types of sample information listed for each sample (two rows above the first row containing sample information).
Specifies the file paths for biomarkers and metrics to be included for interpretation. File names can include symbolic references to the files that depend on the Sample ID or Pair ID:
{pairId}
{sampleId.DNA}
{sampleId.RNA}
When using the workflow scheme file template downloaded from the Configuration page, lines for files that are not uploaded can be deleted. The , Optional
designation can be removed unless the file is an optional file for the pipeline.
The following table shows specific sample visualization files used for IGV. File formats include .bam and .bam.bai. For more information, refer to IGV Visualizations. Under alignment Files, the , Optional
designation can be removed unless the file is an optional file for the pipeline.
The following example shows the custom pipeline configuration process using Local Run Manager TruSight Oncology 500 Analysis Module v2.2. For details on this process, refer to Custom Pipeline Configuration.
Uploaded data is organized as cases that provide details about the sample. A case is a secondary analysis result that has been imported and annotated.These files include VCF files for genetic variants (or CSV files for TruSight Oncology 500 RNA Fusion variants). The cases page lists all cases for your account or workgroup. The following files can be uploaded, but are not required:
BAM files
JSON, TSV, and CSV files for TMB, MSI, and GIS biomarkers or for QC metrics
Make sure that the sample sheet is included in the secondary analysis results folder. The following example shows the structure of the [Data]
section of the sample sheet:
Using this example, Connected Insights creates the following cases:
Open the secondary analysis results folder and find the files that must be identified in the workflow schema file. The following example shows the secondary analysis results folder structure:
For more information, refer to Create a Workflow Schema File in Custom Pipeline Configuration.
The following example shows the workflow schema file structure:
❗ If
, Optional
is after the file name, then Connected Insights uploads the file if it is available or moves on to the next available file.
File
Compatibility
gisFile
JSON containing genomic instability score data.
msiFile
JSON containing microsatellite instability data.
tmbFile
JSON or CSV file containing tumor mutational burden data.
purityPloidyFiles
TSV or VCF file containing purity and ploidy estimates.
snvFiles
VCF files containing small variant calls.
cnvFiles
VCF files containing copy number variant calls.
svFiles
VCF files containing structural variant calls. The structural variant caller can also call longer small variant insertion/deletion/delins events and can duplicate calls from the small variant caller.
rnaSpliceFiles
VCF files containing RNA splice variant calls.
rnaFusionFiles
VCF files containing RNA fusion variant calls.
metricsQCFile
TSV file containing QC metrics data.
File
Compatibility
dnaBamFile
BAM file for the DNA alignment (under alignmentFiles).
dnaBaiFile
BAI file for the DNA alignment (under alignmentFiles).
rnaBamFile
BAM file for the RNA alignment (under alignmentFiles).
rnaBaiFile
BAI file for the RNA alignment (under alignmentFiles).
coverageFiles
TSV file containing coverage data (under visualizationFiles).
balleleFiles
BEDGraph containing b-allele data (under visualizationFiles).
Case ID
Workflow Type
Disease
Sample ID
Sample Type
Control-Case
DNA and RNA
Malignant tumor of unknown origin (SNOMEDCT ID255052006)
DNA_Control RNA_Control
DNA RNA
Lung_001
DNA and RNA
Non-small cell lung cancer (SNOMEDCT ID 254637007)
Lung_DNA_001 Lung_RNA_001
DNA RNA
Breast_002
DNA
Malignant tumor of breast (SNOMEDCT ID 254837009)
Breast_DNA_002
DNA