The approach to sequencing genetic material has evolved over the decades. When next generation sequencing (NGS) arrived in the market at the beginning of this century, it replaced the slow and expensive Sanger sequencing, allowing several DNA fragments to be read simultaneously. Much of the world’s NGS has been performed by Illumina, which has historically produced about 90% of the world’s genomic data. Various sequencers have attempted to topple Illumina’s dominance, but Illumina continues to lead the genomic sequencing space. Now with the entry of Roche’s AXELIOS 1, could it break Illumina’s long-standing hold over the market?
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Roche’s AXELIOS 1 debuts in market: what’s behind this next generation DNA sequencing technology?
AXELIOS 1 hit the market late last month in hopes of addressing “critical bottlenecks” in genomics and clinical research, according to the Swiss pharma giant. Based on Roche’s SBX technology, the sequencer is designed to produce quick and accurate single-molecule analysis. SBX converts DNA into what Roche calls Xpandomer molecules, which are synthetic surrogate polymers that help overcome the spatial limitations of standard nanopore sequencing as genetic material get converted into these molecules.
These surrogate polymers are much larger in comparison to DNA, and therefore, can be more efficiently read with a nanopore. Electrical current that is passed through the pore helps identify the four nucleobases adenine, guanine, cytosine, and thymine. The sequencing typically done on unmodified DNA creates noisy signals, which Roche’s surrogate polymers into the system, circumvents.
“Our approach to efficiently sequencing DNA was to not sequence DNA,” Mark Kokoris, head of the team behind Roche’s technology, said in a webinar last year. It is to read these surrogate polymers instead.
The company engineered enzymes to convert the DNA into Xpandomers as accurately as they can to behave somewhat like an accordion, stretching out to around 50 times as long as a DNA strand.
The brains behind SBX technology was Stratos Genomics, founded in Washington in 2007. It was then acquired by Roche six years ago to prepare for its launch. The chief executive officer (CEO) of Roche Diagnostics, Matt Sause, believes it will be a “disruptive sequencing solution.”
“These attributes, combined with our high level of cost efficiency, will enable the sequencing community to develop applications that previously were not feasible,” said Sause. “Additionally, in the future, AXELIOS 1 has the same potential to enable the next generation of clinical applications and unlock new frontiers in personalised healthcare.”
But how disruptive can it be when DNA giant Illumina has commanded the industry for decades? What Roche’s surrogate polymers do to bypass noisy signals in nanopore sequencing is not even a concern for Illumina as it utilizes short-read Sequencing by Synthesis (SBS) technology. Instead of employing molecules like Xpandomers to unravel under a nanopore, it uses fluorescent labels to recognize single bases and determine their precise order.
Illumina’s next generation DNA sequencers drive market
One of its most popular sequencers is NovaSeq X Plus, which came out four years ago. With an output of up to 16 Tb per run, it can sequence around 20,000 genomes a year and was created to meet the needs of large commercial service providers. It is integrated with Illumina’s DRAGEN software platform, which achieved a 99.9% accuracy score using the Precision FDA Truth Challenge v2 – a benchmark project to evaluate the accuracy of softwares that decode DNA.
While NovaSeq X Plus costs $1,250,000, in contrast, its compact benchtop sequencer MiSeq i100 is about $49,000. This is designed for everyday lab use and rapid turnaround projects like pathogen detection and targeted sequencing. Both these sequencers are thought to be among the best sequencers of 2026.
As Illumina dominates 70% of the market, analysts believe that it will be hard for Roche to unseat it. Since most labs have already incorporated Illumina workflows, switching to another provider would be much more expensive and riskier, giving the company a sticky customer base, according to a report by Ad Hoc News. Plus, it has partnered with a number of big pharmas as well as projects funded by the National Institutes of Health (NIH), including a $14.4 million grant to pilot the integration of whole genome sequencing into existing state newborn screening systems in collaboration with medical institutes.
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However, with Axelios priced at $750,000 – significantly lower than Illumina’s NovaSeq X series – Roche is expected to carve out its market share rather than notably shake things up. It expects to sell around 100 machines this year to generate more than 1 billion Swiss francs ($1.1 billion) in the long run.
Failed takeovers and near-monopolies
The Swiss pharma company has eyed Illumina’s monopoly for a while now. Back in 2012, Roche abandoned a hostile takeover of the American genomics company in a $6.8 billion bid. Having declined to pay a higher price, Roche set out to partner and invest in the $7.3 billion gene-sequencing market.
Meanwhile, Illumina, on the other hand, failed to acquire California-based PacBio following regulatory pushback. The Federal Trade Commission in the U.S. quashed Illumina’s plans of a $1.2 billion buyout on the grounds of violating antitrust laws back in 2020. Today, PacBio’s Revio system is widely adopted by research institutions as it combines long-read HiFi sequencing – with an accuracy rate of 99.9% – with industrial-level throughput and a much lower cost-per-genome. Up to 1,300 human genomes can be sequenced annually with high completeness and it is regarded as the “best high-end” choice for a sequencer, according to a report by LabX.
Similarly, California-based Element Biosciences’ AVITI24 is an up-and-coming rival of Illumina’s NGS technology. Founded by Illumina scientists about a decade ago, the company developed its AVITI24 sequence, which has a high throughput of up to 3 billion reads per run and is significantly cheaper than Illumina’s platforms. When AVITI24 hit the market in 2024, the startup claimed that companies that bought its gene sequencer would save around $1.5 million in three years.
Oxford Nanopore: a worthy challenger?
Meanwhile, Oxford Nanopore’s market share has grown by 28% annually over the past five years, Market Intelo reported. While it has a relatively small market share in the genomics sector, it is known for its long-read sequencing capabilities, particularly PromethION and the portable MinION.
“The portability of this nanopore sequencing device is actually quite an important lead for it in general in the sequencing landscape because for the first time you could actually sequence in the field on the go,” said Toon Swings, technology expert at the Vlaams Instituut voor Biotechnologie (VIB) in Belgium. “The nanopore sequencer just needs a USB port to be powered, so it allows you to do on-field sequencing. There are very nice applications, for example, in the rainforest or in the desert, where you can sequence plant species, or you can sequence bacteria, you can do diagnosis; all kinds of things.”
The DNA goes through the nanopore, and the bases are read as electric current passes through. But the error rate is higher especially compared to Illumina’s high accuracy heavyweights. Although things are looking up, as a recent study found that the MinION sequencer “achieved high accuracy and identity levels of at least 90%” when sequencing phage DNA and Escherichia coli DNA.
In China, however, Illumina has faced turbulence over geopolitical tensions. When U.S. President imposed tariffs on Chinese exports, China retaliated by slapping sanctions. While the import ban on Illumina’s sequencers has been lifted, it remains on the country’s ‘Unreliable Entities List’. While it once enjoyed a near-monopoly in China, since trade wars with the U.S., local competitors in the region have risen, including BGI Genomics and its subsidiary MGI Tech.
Although Roche’s AXELIOS 1 adds to the growing number of sophisticated approaches to gene sequencing, at present, the bulk of market shares remain skewed towards Illumina. How much of an impact AXELIOS 1 will make, only time will tell.
