DRAGEN Array Cloud Analysis

DRAGEN Array Cloud Analysis Overview

DRAGEN Array Cloud utilizes the user-friendly graphical interface of BaseSpace Sequence Hub to simplify DRAGEN Array analysis setup and kickoff. Optional integration with the iScan System allows data to be streamed directly from the instrument to the cloud platform. Analysis data is stored on the Illumina Connected Platform providing secure storage for both microarray and sequencing data.

Getting Started

The following prerequisites are needed to get started with DRAGEN Array Cloud:

• Illumina Connected Analytics subscription: An ICA Basic, Professional or Enterprise subscription can be used which include access to BaseSpace Sequence Hub. Follow the Illumina Software Registration Guide to register the software.

• Workgroup setup: Administrator must create a workgroup before users can log in. Using a workgroup allows all members of the workgroup to share access to resources, analyses, and data. Learn more about managing a Workgroup.

  • Designating a workgroup as ‘Collaborative’ allows projects to be shared with collaborators or Illumina Tech Support to assist with troubleshooting. To create a collaborative workgroup, select the Enable collaborators outside of this domain checkbox during workgroup creation.

• Software consumables: iCredits can be purchased for storage on the cloud platform and analysis pipelines with a compute charge. Per sample analysis can be purchased for relevant pipelines as listed in section Applications. Follow the Example 3: Configuring Software Consumables (iCredits or Sample Analyses) in the Illumina Software Registration Guide to register the software consumables.

• [Optional] iScan integration: The iScan System is integrated with Illumina Connected Platform and can send IDATs for further analysis. The iScan System must be running iScan Control Software version 4.2.1 or later.

  • Instructions to Use Illumina Connect Analytics (ICA) with the iScan System

  • Troubleshooting iScan integration

• EULA acceptance: Accept all necessary End User License Agreements in BaseSpace Sequence Hub before scanning begins.

• Internet connection: For uploading product files or IDATs, a network connection 1 GbE or faster is recommended.

Running Analysis

Before beginning analysis, ensure workgroup context is being used so analysis can be viewed by all members of your workgroup. The name of your workgroup should appear in the top right corner.

Use the following steps to run the Microarray Analysis Setup on BaseSpace Sequence Hub:

1. Select the Runs tab

2. Select New Run

3. Select Microarray Analysis Setup

4. Enter the Analysis Name (Figure 1)

1. Use the Select Project link to choose the project for your output files To select an existing project, click the radio button next to the desired project name. You can also create a project by clicking the New button in the project selection window.

2. Select the Type of Analysis Further detail of each Type of Analysis is available in section Applications. Note: For PGx CNV calling, it is recommended that 96 or more samples passing LogRDev <= 0.2 are included in the analysis. For PGx star allele calling, it is recommended to QC the samples and review the samples that have Log R Dev > 0.2, call rate < 0.99, or TGA Control probe < 1.0 to assess the reliability of the analysis. These metrics are provided in the genotyping sample summary file (gt_sample_summary.csv). For more details, see the explanation for the local analysis.

3. (Optional) Create a custom configuration via the "Add Custom Configuration" option in Configuration Settings. Custom configurations must be assigned a name and product files can be uploaded or selected (Figure 2). For product file names, they should only include alphanumeric characters and underscores, no spaces. Custom configuration options vary by Type of Analysis including:

• DRAGEN Array – Genotyping provides flexibility for turning off/on specific output files and adjusting GenCall score cutoff. Its recommended to turn off VCF output for non-human species and Final Report output for large sample numbers.

• DRAGEN Array – Cytogenetics analysis provides options to adjust thresholds as detailed on the DRAGEN Array Cytogenetics Analysis page. The GTC and SNV VCF options listed on that page are configured in the "Add Custom Configuration" window at the bottom under "Additional Output Options".

• DRAGEN Array - Cytogenetics analysis + Emedgene interpretation shares the same options detailed on the DRAGEN Array Cytogenetics Analysis page.

• DRAGEN Array – Methylation – QC provides options to adjust thresholds as detailed on the DRAGEN Array Methylation QC page.

• DRAGEN Array – PGx – Star allele annotation provides an option to change the default metabolizer status database used from CPIC to DPWG.

1. Select your preferred option in the Configuration Settings drop-down menu Configuration setup will vary based on the Type of Analysis selected. More details are available in section Applications.

2. Select Next

3. Select either Import Sample Sheet, Select BeadChips, or Import IDAT Files (Figure 3)

• Import Sample Sheet presents a link to upload sample sheet. Users may download a template sample sheet by selecting the Download Template link.

• Select BeadChips allows users to select BeadChips from the displayed list of available BeadChips. If selecting specific samples within the BeadChip is desired the Import Sample Sheet option should be used.

• Import IDAT Files allows users to upload the IDAT files from a local folder to the cloud platform for use with the current and future analyses by users within the same workgroup.

1. Select Launch Analysis

View Outputs

1. On the Analyses tab, view the analysis status, e.g., initializing or complete.

2. After the analysis is complete, select the analysis and select the Files tab.

3. From the Files tab, select the Output folder.

Manage Data

The data management tab allows you to view and manage all your scanned IDAT files in the cloud. Before viewing, ensure workgroup context is being used so all data available your workgroup can be seen. The name of your workgroup should appear in the top right corner. For more information, see BaseSpace Data Management.

Troubleshooting and Additional Support

Troubleshooting iScan integration

The firewall protects the iScan control computer by filtering incoming traffic to remove potential threats. The firewall is enabled by default to block all inbound connections. Keep the firewall enabled and allow outbound connections.

For the instrument to connect to BaseSpace Sequence Hub, you will need to add regional platform endpoints and instrument specific endpoints to the allow list on your firewall. Regional endpoints and further detail can be found in Security and Networking for Illumina instrument control computers.

The following table shows the applicable endpoints for the iScan.

Some notes on IDAT fail status: iScan will mark certain samples with a FAIL status if the registration quality is too poor for that particular section. Selected samples that are marked with FAIL status will be excluded from analysis and there would be no results for that sample, even though IDATs are generated. The registration quality can be found in the metrics.txt file. More information on that file can be found in the iScan documentation.

Some notes on Illumina LIMS: If using Illumina LIMS integration with the iScan, it's possible to set sample names that will be encoded in the IDATs and downstream will show up in analysis output files like VCFs instead of the sample ID (Sentrix Barcode + Position). This can cause issues with Emedgene integration for cytogenetic analysis as that sample name is used as a unique identifier. So it is highly recommended to not use that feature in Illumina LIMS to ensure the sample names remain unique throughout the various analyses.

Some notes on running a semi-custom PGx product: Detailed notes on running this analysis for local can be found here. But for cloud, a workaround is necessary because the semi-custom product samples are filtered from the beadchip table. Here are the steps for that workaround:

1. Select an existing commercial product configuration (e.g., GDA_PGx-8v1-0_G4 - GRCh38).

2. Kick off an analysis using the Import Sample Sheet option for the semi-custom product samples.

Sharing a project

Project sharing allows a user to share files with users outside the workgroup for collaboration or with Illumina Tech Support for troubleshooting. To share a project on BaseSpace Sequence Hub, first set the Workgroup type as ‘Collaborative’ during Workgroup setup, and then use the following steps to obtain a link to your project. The project can then be accessed by anyone with the link. All files in the project are shared.

1. Navigate to the Projects tab

2. Click the button next to the desired project

3. Select the Share button above to list (Figure 3)

4. Select the Get Link Option to Activate a link for the project

5. Copy the link and send it to the desired recipient(s)

Additional Notes:

• The project owner maintains ownership and write access. If project owner deletes the data, the collaborators lose access to it.

• Either sending or receiving domain must be collaborative. See "Workgroup setup" here.

• Must be in the same AWS regional instance (i.e."Data cannot be transferred directly between instances, however you can download and share data separately." )

• For Enterprise domains, use this same method (share-by-link, not share-by-transfer)