Connected Insights v5.0: Integration of AI models, interactive visualizations, and new variant curation capabilities

Connected Insights version 5.0 unlocks key new functionality for somatic oncology research applications, including AI algorithms to support variant prioritization and oncogenicity prediction, as well as enriched visualization and curation capabilities. See the latest software release in action by requesting a demo by a technical specialist.

Innovation is at the core of what we do at Illumina. Our newest release of Connected Insights v5.0 equips our somatic oncology NGS customers to perform variant interpretation and research report generation with more confidence and efficiency. Breakthrough Illumina proprietary algorithms including PrimateAI-3D and new curation technology are now available at our customers’ fingertips. Additional features such as an interactive Circos plot visualization and multi-version support (for software version updates to fit on your schedule) are bundled into the release of Connected Insights v5.0 , making this a significant leap forward in functionality.

Building on version 4.0 released in May, Connected Insights v5.0 highlights include:

• Integration of PrimateAI-3D (in addition to SpliceAI) algorithms into automated oncogenicity prediction scoring framework for variants

• Newly added data visualizations, including interactive Circos plot and enhanced fusion plots, providing alternative views for exploring large and complex biological events (structural variants, fusions)

• Enhancements to My Knowledge Base (MyKB) curation capabilities, now creating a complete variant curation environment, allowing for roles-based permissions around creating, reviewing, editing, approving, and filtering variant assertions and related information

Let’s jump into the details of a few of the new capabilities included in Connected Insights v5.0:

Integration of PrimateAI-3D

Our previous release, Connected Insights v4.0, introduced new functionality for automated, guidelines-based oncogenicity classification of variants. Connected Insights v5.0 newly incorporates the latest and greatest PrimateAI-3D and SpliceAI algorithms as part of its oncogenicity prediction scoring framework, empowering users to achieve greater variant classification accuracy and confidence in their insights. PrimateAI-3D and SpliceAI, developed by Illumina’s AI laboratory and academic collaborators, are pathogenicity prediction scores based on algorithms that identify disease-causing variants with superior accuracy as compared to all other classifiers tested (Gao et al., Science, 2023; Jaganathan et al., Cell, 2019).

Access an overview and webinar, along with the peer-reviewed journal articles to learn more - and stay tuned to this exciting area of innovation for Illumina and our community of innovators!

New Visualizations: Circos and Fusion Plots

Latest advances in NGS are enabling better detection of large and complex biological events, such as fusions and structural variations, which are important in oncology variant analysis. Innovations within the field are now going beyond, enabling the detection, interpretation, and visualization of less known events which may be critically tied to oncology applications. Version 5.0 of Connected Insights builds on previous releases by introducing an interactive Circos plot and new fusion plot enhancements.

Created in 2009 by Martin Krzywinski and colleagues at Canada's Michael Smith Genome Sciences Centre and the British Columbia Cancer Research Center, the Circos plot is a visualization tool with widespread application in comparative genomics. Circos plots map variation in genomic data across chromosomes, all within a single view.

Connected Insights v5.0 users can now access Circos plots as an additional option to existing linear genome views under the visualization tab.

The latest release of Connected Insights additionally offers improvements to visualizations of fusions, bringing additional biological context to enable even more insights. As part of v5.0, users can view information on exons, directionality, and maintenance of frame within each relevant fusion plot.

Enhanced curation capabilities within MyKB™

Storing, editing, and sharing variant assertions is a critical component of any oncology bioinformatics workflow. Connected Insights provides My Knowledge Base (or ‘MyKB’), which is a lab’s private, unified knowledge base, for curating all previously interpreted variants, whether through one-off single-sample interpretations or batch uploads of past variant assertions.

Version 5.0 of Connected Insights now enhances MyKB functionality by enabling users with role-based permissions to curate variants independent from samples, with the ability to view, search, edit, approve, archive, view history, and collaborate on assertions all within the lab’s private, central hub. Latest MyKB functionalities introduced allow our customers to see the version history and past cases associated with each variant assertion.

MyKB enables:

• Batch upload past variant assertions
• View list of reports with an assertion
• Create and edit assertions from Biomarker page in a case
• View, search and filter existing variant assertions
• View assertions details (date, author, previous versions, approval status)
• Collaborate on variant interpretation – draft and approved assertions
• Edit and archive assertions from My Knowledge Base page

Other key features

Additional Connected Insights v5.0 features include:

• Multi-version support– Assess the latest version in our newly introduced staging environment prior to transitioning to a production environment. Elect to independently update each workgroup (staging, training, production) to a higher software version as needed.

• Manual data upload from ICA– In addition to automated case creation and VCF data ingestion, create cases manually as needed by browsing to existing analysis results in Connected Analytics.

• Case owner management– Assign cases to users in a workgroup for better data management.

• Audit logs– Search, filter, and export audit logs for a specific case analysis directly from the Connected Insights interface for increased efficiency and greater alignment with institutional compliance guidelines.

Learn More

Your purpose drives our platform development. Packed with efficiency and usability gains, the latest release of Connected Insights v5.0 enables oncology customers to go further with insights and efficiency. Visit the Connected Insights webpage to learn more about our technology and speak with a Technical Specialist. We hope to serve you as part of this dynamic and growing community!

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

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