Updated Oct 2, 2022 - Science

There's a new competition for faster, cheaper DNA sequencing

hand in a fist holding DNA helix

Illustration: Aïda Amer/Axios

Competition is intensifying in the DNA sequencing industry, which has long been dominated by sequencing behemoth Illumina.

Driving the news: Illumina, which has an estimated 80% share of the global gene sequencing market, unveiled a new line of instruments today that it says will cut the cost of genome sequencing — the latest in a flurry of announcements from an industry in pursuit of faster and cheaper offerings.

What they're saying: "It's Illumina's response to the competition," says Jay Shendure, a professor of genome sciences at the University of Washington.

  • Element Biosciences, a startup with a benchtop sequencer already on the market, announced updated specifications this week that CEO Molly He says will support its market play to offer researchers high-quality genome sequencing faster.
  • Earlier this year, another startup, Ultima Genomics, said it would start to ship a sequencer that can generate a genome for $100 next year.

Why it matters: DNA sequencing powers research in biology and medicine. It enables doctors to monitor for cancer recurrence, epidemiologists to track COVID case levels, and vaccine developers to know their targets. It's also a critical tool for researchers trying to deliver on the promise of medical care that detects disease earlier and tailors treatments.

  • All of those applications and aspirations are pushing the industry to offer less expensive, faster and more accurate sequencing.
  • "It's the way we measure things in biology," Shendure says. "For a lot of science, [the cost of sequencing] is like the price of gas."
  • And the cost — about $600 to sequence a human genome today, according to Illumina — is still limiting for many projects and goals. "It's something a large fraction of the community needs and when someone comes along and says it will significantly cut the price of gas, it is a big deal," he says.

Details: Illumina says its new sequencers, NovaSeq X and NovaSeq X Plus, are twice as fast as the existing NovaSeq sequencer that is widely used across industry and academic institutions.

  • The roughly $1 million sequencers, which will begin to be shipped in 2023, can sequence a human genome for less than $240 — the company's "biggest step forward" in its chemistry since first launching a sequencer 17 years ago, Illumina CEO Francis deSouza told me earlier this year. Sequencing a human genome cost $100 million 21 years ago.
  • Illumina says its new system can sequence more than 20,000 genomes per year compared to about 7,500 on their current system.
  • Worth noting: Generating and analyzing sequencing data leaves a hefty carbon footprint. Illumina says the new sequencers use less plastic and packaging, and can be shipped outside the cold chain.

The impact: Less expensive genome sequencing could enable many more genomes to be sequenced and could help address a lack of diversity in genetic datasets, an issue that currently leads to limited understanding and treatment of diseases.

  • On the other end of the spectrum, samples could be sequenced multiple times in search of rare genetic variants involved in cancer.

Answering different questions in science and medicine will call for different requirements for the speed and accuracy of sequencing, Shendure says.

  • Different companies are emerging to occupy these needs and niches — and to give researchers and clinicians options other than Illumina.
  • Researchers who don't have large numbers of samples to be sequenced can have to wait for them to be processed alongside other samples. He, of Element, says scientists "can get this economy on our instrument." She says the company will deliver three genomes for $1,680.

The big picture: It isn't just a homegrown competition.

  • MGI, a subsidiary of China's own biotech behemoth BGI, recently got the green light to sell its sequencers in the U.S. in a deal with Illumina.
  • The same month, Illumina also opened its first manufacturing facility in China.

Editor's note: This story has been updated to include more information about how many genomes Illumina's new sequencers can generate each year.

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