Integrated DNA Technologies Introduces End-to-End Oncology Research Workflows Optimized with Illumina, Inc. Software for Faster Insights
Integrated DNA Technologies (IDT), a Danaher company and a global leader in genomics solutions, has announced a strategic collaboration with Illumina, Inc. to enhance somatic oncology research workflows through a more tightly integrated sequencing and analysis ecosystem. The partnership connects IDT’s widely used next-generation sequencing (NGS) library preparation technologies with Illumina’s DRAGEN™ secondary analysis platform, aiming to accelerate the path from raw sequencing data to actionable biological insights.
The collaboration is designed to simplify and standardize the analytical steps required after sequencing, particularly in oncology research where sample quality, speed, and reproducibility are critical. By integrating wet-lab and bioinformatics workflows, the companies aim to reduce the computational burden on researchers and improve the consistency of variant detection across large-scale studies.
Building an Integrated Workflow for Oncology Research
At the core of the collaboration is the integration of IDT’s xGen™ FFPE and circulating cell-free DNA (cfDNA) library preparation workflows with Illumina’s DRAGEN secondary analysis system. These IDT platforms are already widely adopted in oncology research laboratories and support hundreds of thousands of samples each year, including challenging clinical specimens such as formalin-fixed paraffin-embedded (FFPE) tissue and low-input liquid biopsy samples.
FFPE samples are commonly used in cancer research and diagnostics but often present technical challenges due to DNA degradation, chemical modifications, and fragmentation. These limitations can introduce noise and reduce the accuracy of genomic analysis if not properly addressed.
To overcome these challenges, the newly developed DRAGEN Somatic for IDT Custom Panels workflow introduces an optimized analysis pipeline specifically designed for FFPE-derived sequencing data. The system includes a newly introduced low-quality FFPE mode that enhances variant detection accuracy in degraded samples, helping researchers recover more reliable insights from difficult clinical material.
By connecting IDT’s library preparation chemistry with Illumina’s high-performance computational infrastructure, the integrated workflow aims to deliver a more seamless transition from sample preparation to data interpretation.
Accelerating the Path From Sample to Insight
A key objective of the collaboration is to reduce the time and technical effort required for researchers to move from sequencing output to meaningful biological conclusions.
Traditionally, NGS workflows involve multiple separate steps, including library preparation, sequencing, alignment, variant calling, and downstream interpretation. Each step often requires different tools, software environments, and manual intervention, increasing the risk of inconsistencies and delays.
The new integrated workflow streamlines this process by embedding analysis directly into the sequencing ecosystem. Once samples are prepared using IDT’s xGen FFPE or cfDNA workflows and sequenced, data can be processed directly using the DRAGEN Somatic for IDT Custom Panels application within Illumina’s software environment.
This integration is designed to reduce hands-on computational work while increasing the speed and reproducibility of results. Researchers can move more efficiently from raw sequencing data to clinically or biologically relevant findings, particularly in somatic oncology studies focused on identifying cancer-associated mutations.
In addition, outputs from the DRAGEN pipeline are compatible with Illumina Connected Insights, Illumina’s flagship variant interpretation system. This compatibility enables streamlined downstream reporting and interpretation of somatic variants, helping researchers translate sequencing results into actionable insights more quickly.
Leadership Highlights Importance of Connected Genomics Ecosystems
Executives from both companies emphasized that the collaboration reflects a broader shift in genomics toward more integrated, analytics-enabled research ecosystems.
Konstantin Fiedler, Vice President and General Manager of Gene Reading at IDT, described the initiative as a step toward transforming how genomic data is generated and analyzed. He noted that modern genomics workflows are increasingly moving toward fully connected systems that combine laboratory and computational processes in a unified environment.
According to Fiedler, the collaboration with Illumina represents a milestone in expanding IDT’s capabilities beyond reagent and library preparation tools into more tightly integrated analytics solutions. He emphasized that researchers increasingly require end-to-end workflows that are not only high-performing but also capable of handling real-world clinical and research samples, including those that are degraded or limited in quantity.
From Illumina’s perspective, Kevin Moore, Vice President of Software Product Management, highlighted the importance of scalable and intuitive data analysis tools in modern oncology research. He stated that collaborations such as this one expand access to Illumina’s broader data analysis ecosystem and support more reproducible and consistent results across laboratories.
Moore further noted that combining IDT’s custom panel technologies with the DRAGEN analysis environment reflects a shared goal of advancing cancer research, biomarker discovery, and precision medicine through improved computational and laboratory integration.
Expanding Support for FFPE and cfDNA Applications
The initial rollout of the integrated workflow focuses primarily on FFPE tissue samples, which remain one of the most widely used specimen types in oncology research despite their technical limitations.
FFPE samples are essential for retrospective clinical studies and biomarker discovery, but they often present degraded DNA that complicates sequencing accuracy. The DRAGEN Somatic for IDT Custom Panels workflow addresses these challenges through specialized algorithms designed to improve variant calling sensitivity and specificity in low-quality inputs.
In addition to FFPE applications, the companies plan to expand the workflow to circulating tumor DNA (ctDNA) and other cfDNA-based liquid biopsy applications. A version of the integrated pipeline optimized for cfDNA targeted sequencing is expected to become available in the coming year.
This expansion is particularly significant because cfDNA-based liquid biopsy approaches are increasingly being used in oncology for noninvasive cancer detection, treatment monitoring, and resistance profiling. However, these applications require highly sensitive and accurate analytical tools due to the low abundance and fragmented nature of tumor-derived DNA in blood samples.
By extending the DRAGEN-IDT integration into cfDNA workflows, the collaboration aims to support a broader range of oncology research applications, from early detection studies to longitudinal monitoring of disease progression.
Two Complementary Platforms for Different Sequencing Needs
While the DRAGEN integration focuses on hybrid capture-based sequencing workflows, IDT also continues to support alternative sequencing approaches through its Archer™ Analysis platform.
For anchored multiplex PCR (AMP™)–based data, Archer Analysis provides a dedicated solution that delivers interpretation-ready results through automated error correction, built-in quality control metrics, and user-friendly visualization tools.
This dual-platform strategy allows researchers to select the most appropriate analytical approach depending on their experimental design and sequencing methodology. Hybrid capture users can leverage the DRAGEN-integrated workflow for high-throughput somatic variant analysis, while AMP-based workflows can rely on Archer Analysis for streamlined interpretation.
Together, these platforms provide flexibility across a wide range of oncology research applications while maintaining consistency in data quality and interpretability.
Enhancing Reproducibility and Scalability in Cancer Genomics
A central theme of the collaboration is improving reproducibility in genomic research. Variability in sequencing analysis pipelines has long been a challenge in oncology studies, where differences in computational methods can lead to inconsistent variant calls and interpretation outcomes.
By standardizing the analysis layer through DRAGEN and tightly integrating it with IDT’s library preparation chemistry, the companies aim to reduce variability introduced by fragmented workflows. This standardization is expected to improve cross-study comparability and support more robust biomarker discovery efforts.
Scalability is another key focus. As genomic datasets continue to grow in size and complexity, researchers require tools capable of handling large volumes of sequencing data without sacrificing performance or accuracy. The DRAGEN platform is designed for high-speed, hardware-accelerated analysis, making it well suited for large-scale oncology studies and clinical research programs.
Supporting the Future of Precision Oncology
The collaboration between IDT and Illumina reflects broader trends in precision oncology, where integrated platforms combining sample preparation, sequencing, and data analysis are becoming increasingly important.
As cancer research moves toward more personalized treatment strategies, the ability to rapidly and accurately interpret genomic data will play a central role in identifying therapeutic targets, monitoring disease progression, and understanding mechanisms of resistance.
By unifying laboratory workflows with advanced bioinformatics tools, the companies aim to support the next generation of oncology research and enable faster translation of genomic discoveries into clinical applications.
Researchers interested in implementing the DRAGEN Somatic for IDT Custom Panels workflow can access additional resources and activation details through IDT and Illumina’s developer platforms, marking the beginning of a more tightly connected ecosystem for somatic cancer genomics.
About IDT
Building from a strong foundation of innovation, expertise, and reliability, Integrated DNA Technologies (IDT), a Danaher company, has evolved from an oligo manufacturer to a leading genomics solutions provider. We work shoulder-to-shoulder with scientific and global health partners to enable genomics breakthroughs at scale. Our vision of enabling researchers to rapidly move from the lab to life-changing advances reflects our ongoing commitment to a healthier, brighter future for all.
For more information about IDT, visit www.idtdna.com and follow the company on LinkedIn, X, YouTube, Instagram and Bluesky.
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About Danaher
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