Unlocking the Covid Code
Scientists can now sequence an entire genome overnight
By Jon Gertner
One day at the New York Genome Center, a researcher named Neville Sanjana told me that he thinks of genetic sequencers not as a typical invention but as a kind of “platform technology.” The phrase resonates among those who study innovation. Such technological leaps are rare. They represent breakthroughs that give rise to “platforms” — cellphones, say, or web browsers — that in time revolutionize markets and society.
The immense value of a platform innovation is related to how it can be adapted for a range of uses that are unforeseen at its inception. It can be like a toolbox, waiting at the back of a closet. What happened with sequencing during the pandemic serves as a good example. Another is Sanjana’s work on new Crispr technologies, which he uses to modify or repair strings of DNA to better understand the genetic basis of human disease. Twenty years ago, when officials at the N.I.H. talked about investing in the future of sequencing, altering the human, plant or animal genome on a regular basis was not something they could have predicted. But Crispr requires Sanjana to constantly evaluate his editing by using sequencers — usually a desktop Illumina model, in his case — to check the results. “It would be impossible to do these experiments otherwise,” he says.
It has been the case historically that platform innovations don’t merely create new applications. They create new industries. And while countless genomics companies have already sprung up, for now just four companies run most of the sequencing analyses in the world. These are Illumina and Pacific Biosciences, based in the United States; Oxford Nanopore Technologies, based in Britain; and China’s BGI Group.
According to the Federal Trade Commission, Illumina controls roughly 90 percent of the market for sequencing machines in the U.S., and by the company’s own assessment, it compiles 80 percent of the genomic information that exists in the world in a given year. It is sometimes described as the Google of the genomics business, not only because of its huge market share but also because of its products’ ability to “search” our complete genetic makeup. In short, it dominates the business. Last year, the firm took in over $3 billion in revenue and about $650 million in net income. In its hunger for expansion, the company has recently made a run of acquisitions. In late September, for example, Illumina announced that it intended to acquire, for $8 billion, a biotech company called Grail, which has created a genomic test that runs on an Illumina sequencer and that an early study suggests can successfully detect more than 50 types of cancers from a small sample of blood. On a recent corporate earnings call, deSouza called Grail and early cancer detection “by far the largest clinical application of genomics we’re likely to see over the next decade or two.”
As the pandemic unfolded, I spoke often to genomics executives about which industries could be transformed by their technologies and how their machines would be deployed in the years to come. One model for the future was built around the strengths of Illumina — big machines like the NovaSeq, with an extraordinary capacity for sequencing, housed in central testing labs (as they are now) and run by specialists. But a very different set of ideas emerges from one of Illumina’s main competitors, Oxford Nanopore. Oxford’s sequencers involve a technology that is electronic rather than optical; it is based on the concept of moving a sample of DNA through tiny holes — nanopores — in a membrane. The device measures how genetic material (extracted from a sample of blood, say) reacts to an electric current during the process, and it registers the letter sequence — A, G, C, T — accordingly. One distinctive feature is that a nanopore device can read longer threads of DNA than an Illumina device, which can be helpful for some applications. It can also give readouts in real time.