Overview

Microarray on BaseSpace Sequence Hub provides cloud-based analysis capabilities for Illumina microarray data. The platform supports genotyping, PGx, cytogenetics and other analyses through DRAGEN Array Applications. It also supports polygenic risk score calculations.

Prerequisites

The following prerequisites are needed to get started:

• 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: Workgroups must be created before login. Using a workgroup allows all members of the workgroup to share access to resources, analyses, and data. Learn more about managing a Workgroup.

  • The workgroup owner must be a member of the workgroup with the "Has Access" role assigned. Do not use the "Has Access + Archive" role.

  • 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 DRAGEN Array Applications and Polygenic Risk Score Software. Follow the Illumina Software Registration Guide (found under Example 3: Configuring the Software Consumables) 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.

Note: Accessioning BeadChips before scanning and starting analysis is no longer a required step and has been automated within the system.

Accessing the Microarray Hub

The Microarray Hub is the central location for managing microarray data and analyses on BaseSpace Sequence Hub. Before using the Microarray Hub, ensure workgroup context is being used so all data and analyses 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 access the Microarray Hub on BaseSpace Sequence Hub:

1. Select the Runs tab

2. Select New Run

3. Select Microarray Analysis Setup

Microarray Hub Tabs

The Microarray Hub contains two tabs:

• Data Management - View and manage scanned IDAT files, and start analyses with data that is ready.

• Planned Analyses - View and manage planned analyses that will auto-launch when sample data becomes available.