For DNA sequencing, this “is the year of the great change,” says Michael Snyder, a systems biologist at Stanford University. Sequencing is central to fields from basic biology to virology to human evolution and its importance continues to grow. Doctors are clamoring to use it for the early detection of cancer and other diseases, and biologists are finding more and more ways to use genomics to study single cells. But for years, most of the sequencing relied on machines from one company, Illumina.
Last week, however, a young company called Ultima Genomics said at a meeting in Orlando, Florida that with new twists on existing technologies, it could provide human genomes for $ 100 apiece, one-fifth of the current rate. Several other companies have also promised faster and cheaper sequencing in the same meeting, Advances in Genome Biology and Technology. This year, key patents protecting Illumina’s sequencing technology will expire, paving the way for more competition, including from a Chinese company, MGI, which announced last week that it will begin selling its machines in the states. United this summer. “We could be on the verge of the next revolution in sequencing,” says Beth Shapiro, an evolutionary biologist at the University of California, Santa Cruz (UCSC).
Most sequencing companies, including Illumina, which controlled 80% of the global market, rely on “sequencing by synthesis”. The DNA to be deciphered is separated into individual strands, which are usually cut into small pieces and mounted on a surface, often a tiny bead, in a container called a flow cell. Each individual strand fragment serves as a template to guide the synthesis of a strand with complementary bases, delivered one at a time to the bead channels. Since each base added has been modified to illuminate, a camera can record where it attaches and then the identity of the corresponding base on the original wire. The steps are repeated until the new strand of DNA is completed.
Ultima simplified the process by spraying billions of DNA-laden beads onto round silicon wafers the size of dessert plates. The nozzles on top of each wafer gently spray the bases and other reagents, which spread thinly and evenly over the wafer as it rotates, reducing the amount of these expensive materials needed. Instead of moving back and forth under the camera, the disc spirals, similar to how a compact disc is played, which speeds up imaging. It is “intelligent engineering [that] it avoids a lot of hydraulic complexes, “says Mark Akeson, a molecular biologist at UCSC. A neural network program quickly transforms the imaging data into a sequence.
The chemistry of sequencing is also different. Only a few bases carry fluorescent tags, reducing costs. In addition, the bases lack the usual stop signal, which ensures that no additional bases dock. Without these “terminators,” the growing chain can sometimes add multiple bases at once, speeding up the process. “Many of these innovations are used elsewhere, but they seem to have come together very well here,” says Jay Shendure, geneticist and technology developer at the University of Washington (UW), Seattle.
Ultima CEO Gilad Almogy and his colleagues demonstrated the potential of the technology in four preprints published in late May on bioRxiv. In one, they and colleagues from the Broad Institute at MIT and Harvard used their machine to sequence more than 224 human genomes already sequenced and found their results on par with previous work. The other three studies showed that the technology can evaluate a single cell’s repertoire of expressed genes, the effects of mutations and epigenetics, chemical modifications of DNA that affect gene activity.
So far, the cost has limited such single-cell studies, causing a research bottleneck. But Snyder found that Ultima’s low-cost approach allowed him to sequence multiple colon cancer cells to document how DNA modification, methylation, changes as colon cancer develops.
In another preprint, Joshua Levin and his colleagues at the Broad Institute tested Ultima technology’s ability to identify active genes in individual blood cells, as indicated by the RNA transcripts of the genes. The team found that Ultima’s machine identified those genes as much as Illumina’s. And, he adds, “It’s a game changer because of the lower cost.”
Florence Chardon, a UW genomics graduate student editing DNA with the CRISPR Genome Editor, is thrilled with this prospect. “The less expensive [sequencing] gets, the more this kind of research is accessible to more laboratories and more people, “he says.
But Lior Pachter, a computational biologist at the California Institute of Technology, has reservations about the new technology. He and graduate student A. Sina Booeshaghi examined one of the most active genes in Levin’s team’s blood cells, a possible cancer biomarker also known for producing a protein that athletes sometimes inject to illegally improve their performance. . Ultima technology sometimes lacked the active gene, Pachter says. The “error rate was very high and performance was very poor”.
The gene has a trait where the same base is repeated eight times and Ultima admits that long repetitions can undermine the accuracy of her reads. Looking elsewhere in the Ultima sequence, Pachter found errors when a base was only repeated three times. He notes that a human genome contains at least 1.4 million of these so-called homopolymers. However, he says, “For some applications, you don’t need perfect sequences.”
Pachter and others also contest the advertised cost of $ 100. That figure only covers the reagents, not the labor, the pre- and post-sequencing steps, and the initial outlay for the machine, the price of which has not been released. While the $ 100 figure is real, it may not be unique – other companies are also promising $ 100 per human genome.
One is MGI, a subsidiary of the Chinese sequencing giant BGI. MGI’s technology is similar to Illumina’s, but increases accuracy by adding all four bases at the same time as it sequences DNA. To track which bases are incorporated, it uses antibodies, which are brighter and less expensive than fluorescent dyes. Illumina also promises lower costs and introduced new chemicals during the meeting to increase accuracy and flexibility.
In order for this deal to be realized, Ultima and MGI both require filling their capacity sequencers with hundreds of genomes. But high-throughput sequencing “isn’t always good for clinical practice, even if it’s good economics,” says Greg Elgar, a genome biologist at Genomics England, because sometimes a doctor needs genome analysis from a or a few people. Other companies with new flow cells and chemicals can economically sequence a small number of genomes. At last week’s meeting, Molly He, CEO of Element Biosciences, reported that the company is now shipping over-the-counter sequencers capable of sequencing three human genomes at a time, at a cost of $ 560 each. Another company, Singular Genomics, also promises bench-top technology that doesn’t require high productivity for cost savings.
These machines, like those of Illumina, MGI and Ultima, all decipher short pieces of DNA. But for the past 7 years, two companies, Pacific Biosciences and Oxford Nanopore Technologies, have been working on sequencing “long reads,” thousands of bases long, that leave fewer partial sequences to put together into a complete genome. The technologies “can sequence the native DNA molecule, in all its glory,” says Elgar. They have struggled with low accuracy and high cost, but he says they are about to become practical tools.
Don’t count sequencing giant Illumina just yet. His scientists “probably kept a couple of cards in their pockets” to maintain their strong position in the market, says Albert Vilella, a bioinformatician and genomics consultant in Cambridge, England. However, Illumina faces unprecedented competition, he adds. “Time to watch the [DNA sequencing] landscape with new eyes “.