Illumina’s constellation tech shows promise in GeneDx rare disease study

SAN DIEGO - Illumina, Inc. (NASDAQ:ILMN), a $14 billion market cap genomics leader with a robust 68% gross margin and $4.28 billion in annual revenue, announced Wednesday that GeneDx is piloting its constellation mapped read technology to identify difficult-to-detect genetic variants associated with rare diseases. According to InvestingPro analysis, the company maintains profitable operations with moderate debt levels, though its shares have declined 40% year-to-date.

In a study of 160 DNA samples from individuals with known genetic conditions, GeneDx compared Illumina’s constellation technology against established methods including long-read sequencing, arrays, and multiplex ligation-dependent probe amplification. According to the company’s statement, the technology accurately identified complex variants including repeat expansions and structural variants.

The pilot specifically demonstrated success in detecting variants in genes associated with conditions such as myotonic dystrophy, spinal muscular atrophy, chronic granulomatous disease, and mosaic aneuploidy, which can be challenging to identify using traditional short-read sequencing methods.

"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," said Joe Devaney, GeneDx’s Director of Laboratory Innovation, who presented the findings at the American Society for Human Genetics Annual Meeting in Boston.

Constellation technology builds upon Illumina’s sequencing-by-synthesis chemistry and features on-flow-cell library preparation that eliminates manual steps. The system extracts long-distance data from neighboring clusters to accurately map homologous or repetitive regions of the genome.

The technology was first introduced at the 2024 ASHG conference, with commercial availability planned for the first half of 2026 for the NovaSeq X Series platform.

The pilot study evaluated multiple sample types, including buccal, blood, and chorionic villus samples, demonstrating the technology’s flexibility across different specimen sources.

This announcement comes as Illumina continues to expand its genomic capabilities while facing competition in the sequencing market. The information in this article is based on a press release from Illumina.

In other recent news, Illumina Inc. has reported its second-quarter 2025 earnings, exceeding analysts’ expectations with an earnings per share (EPS) of $1.19, compared to the forecasted $1.01. The company’s revenue also slightly surpassed predictions, reaching $1.06 billion against the expected $1.05 billion. In addition to its financial performance, Illumina announced the formation of BioInsight, a new business unit dedicated to advancing data analytics in life science research and pharmaceutical development. This new division will be led by Rami Mehio, who was previously in charge of Illumina’s Global Software & Informatics team.

Furthermore, Illumina has entered into collaborations with multiple global pharmaceutical companies to develop companion diagnostics for KRAS biomarkers using its TruSight Oncology Comprehensive genomic profiling test. These partnerships aim to broaden claims for KRAS alterations, which are significant in cancer diagnostics. Meanwhile, BioStem Technologies appointed Brandon Poe as its new Chief Financial Officer, with Poe having extensive experience, including a previous role at Illumina as Vice President of Finance. These developments highlight Illumina’s ongoing efforts to enhance its capabilities and partnerships in the life sciences sector.

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