Illumina constellation mapped read technology uncovers hard-to-see genomic insights in GeneDx pilot

Rhea-AI Summary

Illumina (NASDAQ: ILMN) said GeneDx piloted its emerging constellation mapped read technology on 160 DNA samples and reported improved detection of hard-to-map variants versus orthogonal methods. The pilot identified repeat expansions (DMPK), SMN1 events, NCF1-related variants, complex structural variants, and mosaic aneuploidy across blood, buccal, and prenatal samples.

Constellation uses on-flow-cell long molecules with proprietary informatics to resolve homologous and repetitive regions. A commercial product is planned for H1 2026. GeneDx results were presented at ASHG on Oct 15, 2025.

Positive

• Pilot evaluated 160 DNA samples
• Detected clinically relevant variants in DMPK, SMN1, and NCF1
• Performs across blood, buccal, and prenatal sample types
• Commercial product slated for H1 2026

Negative

• Product launch risks: manufacturing and supplier challenges cited
• Customer adoption uncertainty for newly launched products

Insights

Genomics technology analyst

Illumina's constellation shows promising lab performance in a 160-sample GeneDx pilot and could alter WGS detection of hard-to-map variants.

Illumina deployed its constellation mapped read workflow on GeneDx's NovaSeq X Plus fleet and processed Oct 15, 2025-dated pilot data covering 160 known-disease samples. The pilot reports constellation outperformed orthogonal approaches—long reads, arrays, and MLPA—in detecting repeat expansions, complex structural variants, and other hard-to-map signals in genes such as DMPK, SMN1, and NCF1, plus mosaic aneuploidy. The method combines on-flow-cell long template loading with proprietary informatics to extract long-range mapping from neighboring clusters, reducing manual library prep and validation steps.

The result is materially relevant because it addresses specific diagnostic gaps in rare-disease sequencing. Key dependencies temper enthusiasm: manufacturing scale-up, supply-chain and third-party component risks, and real-world clinical validation across diverse labs. The release itself carries forward-looking caveats about customer acceptance and product manufacturing.

Watch two concrete milestones: the GeneDx presentation at ASHG on Oct 15, 2025 and the first commercially available constellation product slated for release in the first half of 2026. Short-term signals to monitor include independent validation datasets, peer-reviewed performance metrics, and adoption by additional clinical labs. Those items will clarify whether the pilot translates into broader clinical utility and commercial uptake.

Illumina's up-and-coming constellation innovation delivers accuracy, speed, and ease of use in trial by GeneDx

Constellation outperformed orthogonal methods in identifying select difficult-to-map variants

SAN DIEGO, Oct. 15, 2025 /PRNewswire/ -- Illumina, Inc. (NASDAQ: ILMN) today announced that GeneDx, a leader in genetic testing for rare diseases, is piloting Illumina's emerging constellation mapped read technology, evaluating its performance on regions of the genome that traditional short-read technologies historically have not resolved. GeneDx's early results illustrate the ability of constellation to rapidly identify hard-to-detect variants implicated in rare disease. GeneDx's Director of Laboratory Innovation Joe Devaney will present on the company's early experiences with the constellation technology today at the American Society for Human Genetics (ASHG) Annual Meeting in Boston.

"Illumina is unlocking ways to access the most difficult regions of the genome, as we simultaneously lead the industry into a new era of multiomics," said Steve Barnard, chief technology officer of Illumina. "Genomic insights remain critical to advance diagnosis and treatment for many rare and complex diseases, and our constellation technology provides the research insights that enable our customers to tackle these challenging conditions on the platforms they already use."

For the pilot project, GeneDx used its fleet of NovaSeq X Plus Systems with constellation kits to evaluate 160 DNA samples from individuals with known genetic disease. GeneDx compared samples run with constellation to orthogonal methods, like long-read sequencing, arrays, and multiplex ligation-dependent probe amplification. Constellation was able to accurately uncover repeat expansions, complex structural variants, and elusive regions of the genome, demonstrating the technology's ability to meet or exceed the capabilities of established alternative methods.  

Constellation was able to quickly identify difficult-to-detect, biologically relevant variants, including those in:

• DMPK , which is associated with myotonic dystrophy and is caused by large repeat expansions;
• SMN1 , which is associated with spinal muscular atrophy but is difficult to detect based on the highly homologous SMN2 gene;
• NCF1 , which is associated with an inherited immune disorder called chronic granulomatous disease, but is challenging to identify due to highly homologous pseudogenes; and
• Mosaic aneuploidy, which causes some cells to have chromosomal abnormalities. It can cause developmental delays and increase the risk of some childhood cancers.

Deep and rapid insights from whole-genome sequencing can help researchers understand and better identify potential treatments for these hard-to-diagnose conditions. Constellation is emerging as a flexible solution that performs accurately across a variety of sample types—including buccal, blood, and chorionic villus (prenatal) samples—and extraction kits.

"Innovation and patient centricity fuel everything we do at GeneDx," said Devaney. "We're continually looking to advance research and clinical genomics to drive the future of precision medicine and better health outcomes for all. The level of detail we can achieve with constellation provides promising insight into some of the world's most complex and difficult-to-diagnose diseases. By combining speed, simplicity, and scientific rigor, this technology has the potential to transform how we understand rare disease, helping improve how we diagnose and treat patients."

How constellation mapped read technology works

Constellation builds on Illumina's industry-leading sequencing-by-synthesis chemistry to unlock long-range genomic insights with unmatched simplicity. Long sequences of unfragmented DNA are applied directly to the flow cell for cluster generation. This on-flow-cell library prep eliminates manual library preparation and enables a streamlined workflow with fewer validation steps. Proprietary informatics extract long-distance data from the proximity of resulting neighboring clusters. This novel data allows for accurate mapping of homologous or repetitive regions of the genome, resolving mapping ambiguities, and resolving complex variant types.

Constellation was first introduced at the 2024 ASHG conference. The first commercially available product based on constellation technology is slated for release in the first half of 2026, compatible with the NovaSeq X Series. 

Joe Devaney will present the results of GeneDx's expanded, 160-sample study with constellation on October 15 at the ASHG Annual Meeting in Boston. His talk, "Mapping the Future of Whole Genome Sequencing with Illumina Constellation Technology," will be held in Room 153ABC from 12:00 PM to 1:00 PM ET. To preregister for access to the replay, follow this link. You can see all of Illumina's multiomics solutions that are in development or commercially available here.

Use of forward-looking statements

This release may contain forward-looking statements that involve risks and uncertainties. Among the important factors to which our business is subject that could cause actual results to differ materially from those in any forward-looking statements are: (i) challenges inherent in developing and launching new products and services, including modifying and scaling manufacturing operations, and reliance on third-party suppliers for critical components; (ii) our ability to manufacture robust instrumentation and consumables; and (iii) the acceptance by customers of our newly launched products, which may or may not meet our and their expectations, together with other factors detailed in our filings with the Securities and Exchange Commission, including our most recent filings on Forms 10-K and 10-Q, or in information disclosed in public conference calls, the date and time of which are released beforehand. We undertake no obligation, and do not intend, to update these forward-looking statements, to review or confirm analysts' expectations, or to provide interim reports or updates on the progress of the current quarter.

About Illumina

Illumina is improving human health by unlocking the power of the genome. Our focus on innovation has established us as a global leader in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets. Our products are used for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments. To learn more, visit illumina.com and connect with us on X, Facebook, LinkedIn, Instagram, TikTok, and YouTube.

About GeneDx

GeneDx (Nasdaq: WGS) is the global leader in rare disease diagnosis, transforming the way medicine is practiced by making genomics the starting point for health, not the last resort. We bring together unmatched clinical expertise, advanced technology, and the power of GeneDx Infinity™ – the largest rare disease dataset – built over 25 years from millions of genomic tests and deep clinical insights. This unparalleled foundation powers our ExomeDx™ and GenomeDx™ tests, giving clinicians the highest likelihood of delivering a timely, accurate diagnosis. GeneDx is shaping the future of healthcare by moving the standard of care from sick care to proactive healthcare. While our roots are in rare disease diagnosis, our commitment extends beyond – growing with the families we serve – as a trusted partner at every stage of life. For more information, visit genedx.com and connect with us on LinkedIn, Facebook, and Instagram.

Contacts

Illumina

Investors:
Illumina Investor Relations
858-291-6421
IR@illumina.com

Media: 
Christine Douglass
PR@illumina.com

GeneDx

Investors:
Investors@genedx.com

Media:
Press@genedx.com

View original content to download multimedia:https://www.prnewswire.com/news-releases/illumina-constellation-mapped-read-technology-uncovers-hard-to-see-genomic-insights-in-genedx-pilot-302584845.html

SOURCE Illumina, Inc.

FAQ

What did Illumina announce about constellation technology on Oct 15, 2025 (ILMN)?

Illumina announced GeneDx piloted constellation on 160 samples, reporting improved detection of hard-to-map variants.

Which hard-to-detect variants did GeneDx find with Illumina constellation (ILMN)?

GeneDx identified repeat expansions in DMPK, SMN1 events, NCF1 variants, complex structural variants, and mosaic aneuploidy.

When will Illumina release the first commercial constellation product compatible with NovaSeq X (ILMN)?

The first commercial product is slated for release in the first half of 2026.

How does constellation mapped read technology work on Illumina systems (ILMN)?

Constellation applies long unfragmented DNA to the flow cell and uses proprietary informatics to extract long-range mapping from neighboring clusters.

Did GeneDx present constellation results at ASHG and when (ILMN)?

Yes; GeneDx presented findings at ASHG on October 15, 2025 in a scheduled talk.