Scientists can now sequence an entire genome overnight

"The sequencing of a virus, much like the sequencing of human DNA from a cheek swab or a drop of blood, is painstaking. Samples are moved along what is essentially an assembly line: “weighed” on exquisitely sensitive “scales” to check the mass of the specimen; bathed with chemical solutions known as reagents; tagged with a “bar code” of genetic material so each sample can be individually tracked. Most of the preparations are about checking the quality of the virus sample and then amplifying its genetic material — in effect, transforming a tiny and invisible amount of the coronavirus extracted from a swab into vast quantities of DNA, all in preparation for being read and analyzed by a device built to do exactly that.

The Illumina NovaSeq 6000 — or “Nova-seeks,” as they’re called are similar to the machines used in China to sequence the coronavirus for the first time. The NovaSeqs are about the size of an office photocopier and have few distinguishing features, apart from a large touch-screen interface and a vent pipe that rises from the back of the device to the ceiling. Each machine costs roughly $1 million; there are about 1,000 of them in the world right now.

The NovaSeqs represent the culmination of about two decades of technological development that in large part began with the Human Genome Project, which was completed in 2003 and funded mainly by the USA National Institutes of Health. The project showed that the human genome — “nature’s complete genetic blueprint for building a human being,” as the N.I.H. describes it — is composed of a sequence of about three billion “base pairs.” These are bonded chemicals coded as A, C, G and T, where A stands for adenine, C for cytosine, G for guanine and T for thymine. The chemical pairs are frequently grouped together on our chromosomes, in about 30,000 information-dense strings, or clumps. The clumps are our genes.

By 2015, the pace of improvement was breathtaking. “When I was a postdoctoral fellow, I actually worked in Fred Sanger’s lab,” Tom Maniatis, the head of the New York Genome Center, told me. “I had to sequence a piece of DNA that was about 35 base pairs, and it took me a year to do that. And now, you can do a genome, with three billion base pairs, overnight.” Also astounding was the decrease in cost. Illumina achieved the $1,000 genome in 2014. Last summer, the company announced that its NovaSeq 6000 could sequence a whole human genome for $600; at the time, deSouza, Illumina’s chief executive, told me that his company’s path to a $100 genome would not entail a breakthrough, just incremental technical improvements. “At this point, there’s no miracle that’s required,” he said. Several of Illumina’s competitors — including BGI, a Chinese genomics company — have indicated that they will also soon achieve a $100 genome. Those in the industry whom I spoke with predicted that it may be only a year or two away. 

These numbers don’t fully explain what faster speeds and affordability might portend. But in health care, the prospect of a cheap whole-genome test, perhaps from birth, suggests a significant step closer to the realization of personalized medicines and lifestyle plans, tailored to our genetic strengths and vulnerabilities. “When that happens, that’s probably going to be the most powerful and valuable clinical test you could have, because it’s a lifetime record,” Maniatis told me.

Yet the biggest difference may be its portability. In 2015, Oxford Nanopore began selling a sampling and sequencing gadget called the Minion (pronounced MIN-eye-on) for $1,000. It is smaller than a small iPhone. The chief executive of Oxford Nanopore, Gordon Sanghera, told me he sees his company’s tool as enabling a future in which sequencing insights can be derived during every minute of every day. Inspection officers working in meatpacking plants would get results about pathogenic infection in minutes; surveyors doing environmental monitoring or wastewater analysis can already do the same. Your dentist might one day do a check of your oral microbiome during a regular visit, or your oncologist might sequence your blood once a month to see if you’re still in remission. A transplantation specialist might even check, on the spot, about the genomic compatibility of an organ donation. “The company’s ethos,” Sanghera says, “is the analysis of anything, by anyone, anywhere.” Indeed, there happens to be a Minion on the International Space Station right now.

The technology, compared with Illumina’s, is considered by most scientists I spoke with to be less accurate, but it has advantages beyond those that Sanghera mentioned. It was the Minion that enabled scientists to test for diseases like Zika without any infrastructure beyond a laptop; more recently, it’s what allowed Esteé Torok and other researchers in Britain to track viral mutations in real time in a hospital. “That ability to do sequencing in the field, even in rural Africa, has opened up possibilities that were never previously even envisioned,” Eric Green, who runs the National Human Genome Research Institute, part of the N.I.H., told me recently."

 If it can be done in an African village, then maybe it can be done in Vilnius? What do you think, ladies and gentlemen recently coming from the Lithuanian countryside?