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Roche Touts 'Good Progress' on Nanopore Sequencer, Stays Mum on Details, Timeline


NEW YORK – Roche said Wednesday that it is making "good progress" developing its nanopore sequencing platform, based on technology it acquired from Genia and Stratos Genomics, but declined to disclose technical details or a launch timeline.

"This is a competitive market; we want to be sure that we have 'dotted our i's and crossed our t's' before we start coming out with further details," Palani Kumaresan, global head of Roche Diagnostics Solutions, told investors during the company's Diagnostics Investor Day in London, which was webcast.

While the performance specs for Roche's nanopore sequencer remain nebulous, the company has been developing the platform with clinical and pharmaceutical markets in mind.

"Simply put, we are not just thinking about the sequencer itself but an end-to-end workflow," Kumaresan said. The company already has a menu of products upstream and downstream of the sequencer on the market, such as a nucleic acid extraction platform and analysis software, he said, and is making sure these will "work seamlessly" with the new nanopore sequencing platform.

"This is really important because some of the fastest-growing subsegments of the sequencing market — the clinical [segment] and the biopharma segment — they really need this end-to-end solution," Kumaresan said.

He noted two key elements of the nanopore sequencing technology: a semiconductor sequencing chip, which Roche obtained through its acquisition of Genia in 2014, and the so-called Sequencing by Expansion, or SBX, chemistry that was originally developed by Stratos Genomics, which Roche acquired in 2020, a move that Kumaresan called "the real pivotal moment."

During the presentation, he provided an overview of the SBX process: DNA molecules are first enzymatically converted into a larger surrogate molecule, called an Xpandomer, that contains reporter molecules representing the DNA bases and generating a strong signal. The Xpandomer, which is more than 50 times longer than the original DNA fragment, then passes through a biological nanopore, with a detector to read out the signal, which is translated back into the DNA sequence.

This mirrors what Stratos had publicly disclosed prior to its acquisition, though it is unclear what improvements Roche has made to the SBX technology since then.

Kumaresan also said the company has been "steadily working to improve" the semiconductor chip from Genia, which will feature 8 million microwells to enable simultaneous sequencing.

Compared with "the nanopore sequencers that are available in the market today," Kumaresan claimed, Roche's new platform will have "a much higher signal-to-noise ratio," leading to improved accuracy.

Meanwhile, compared to traditional sequencing-by-synthesis approaches, Roche's technology supports real-time data generation and analysis and "more flexible run conditions," as well as "very versatile throughput" from low to ultra-high, he said.

Kumaresan also claimed that Roche's sequencer has faster turnaround times than the sequencing-by-synthesis platforms, which he said is beneficial for clinical sequencing. Additionally, given the platform involves no optics, it will be a "much more simplified instrument" with a smaller footprint, allowing for "an attractive cost structure," he noted.

The company, however, did not disclose any performance metrics or show any data to substantiate its claims.

During the presentation, Roche hinted that its nanopore sequencing platform will have short reads, but Kumaresan declined to provide specifics when asked about this by investors during the Q&A session.

"The only thing I would say is, for us, the clinical sequencing market is extremely important; also, the biopharma market is extremely important, and we want to make sure we have the right solutions to address the needs of those customers and also beyond that, as well," he said.

This is not Roche's first attempt to develop an NGS sequencer, as the company has had a long and checkered past with acquisitions and partnerships in the space. In 2017, Roche terminated a collaboration with Pacific Biosciences to develop a clinical diagnostic sequencing platform. Before that, the company attempted, and failed, to take over Illumina in a hostile bid in 2012. Its acquisition of 454 Life Sciences in 2007 also led to the discontinuation of the technology several years later.

While Kumaresan said Roche is "absolutely moving forward in a really good way," it is unclear when the nanopore sequencer will finally come to market. On its presentation slides, the company noted the platform won't come out until "2025+."

"We have spent a lot of time and energy to get it to a place where it is today," Kumaresan said. "Because of the investments we are making, it's not just about how competitive we are when we launch, it has to be a generational technology."