When it comes to DNA sequencing, “it’s a year of great shaking,” says Michael Snyder, a systems biologist at Stanford University. Sequencing is essential from basic biology to virology to human evolution, and its importance is growing. Clinicians are calling for early detection of cancer and other diseases, and biologists are finding more and more ways to study single-cell genomics. But for years, most of the sequencing has been based on the machines of a single company, Illumina.
Last week, however, a young company called Ultima Genomics said at a meeting in Orlando, Florida that with a new twist on existing technology, the human genome could be offered for $ 100, one-fifth of the usual rate. Several other companies also promised faster and cheaper sequencing at the same meeting, Advances in Genome Biology and Technology. This year, the key patents that support Illumina’s sequencing technology will expire, paving the way for more competition, including from China’s MGI, which announced last week that it would start selling its machines in the United States this summer. “We may be on the verge of the next revolution in sequencing,” says Beth Shapiro, an evolutionary biologist at the University of Santa Cruz, California (UCSC).
Most sequencing companies, including Illumina, which controls 80% of the global market, are subject to “synthetic sequencing.” The DNA to be deciphered is divided into a single strand, which is usually cut into short pieces and mounted on a surface — often a tiny specimen — in a container called a flow cell. Each piece of thread serves as a template to guide the synthesis of a thread with additional bases, fitted individually to the bead channels. Since each added base has changed to shine, a camera can record where it is attached, and thus the identity of the corresponding base on the original thread. The steps are repeated until the new DNA strand is formed.
The latter facilitated the process by spraying DNA-filled grains into round silicon wafers the size of billions of dessert plates. The nozzles on each wafer gently pour the bases and other reagents, which spread thinly and evenly throughout the wafer as it rotates, reducing the amount of these expensive materials needed. Instead of moving back and forth under the camera, the disc moves in a spiral, like a compact disc, which speeds up images. “Engineering is smart [that] it avoids a lot of complex plumbing, “says UCSC molecular biologist Mark Akeson. A neural network program quickly converts image data into a sequence.
Sequencing chemistry is also different. Only a few bases carry fluorescent labels, reducing costs. In addition, the bases do not have the usual stop signal, which does not support additional bases. Without these “amateurs”, the growing chain can sometimes add multiple bases at once, speeding up the process. “A lot of these innovations are being used elsewhere, but they seem to have come together very well here,” says Jay Shendure of the University of Washington (UW), a Seattle geneticist and technology developer.
Gilad Almogy, CEO of Ultima, and his colleagues demonstrated the potential of the technology in four prepress releases published in bioRxiv in late May. In one, they and colleagues at MIT and the Harvard Broad Institute used their machine to sequence more than 224 human genomes that were already sequenced, and found their results on a par with previous work. Three other studies showed that technology can evaluate the repertoire of genes in a single cell, the effects of mutations, and the chemical changes in DNA that affect the activity of genes.
To date, the cost of single-cell studies has been limited, and research has affected the bottleneck. But Snyder found that Ultima’s low-cost approach allowed him to sequence multiple colon cancer cells to document how a change in DNA, methylation, changes as colon cancer develops.
In another preprint, Joshua Levin and colleagues at the Broad Institute tested the ability of Ultima technology to identify active genes in a single blood cell as indicated by gene RNA transcripts. The team identified these genes as well as those of the Ultima machine as those of the Illuminati. And, he added, “it’s a game changer because of the lower cost.”
Florence Chardon, a UW genomics student who changes DNA with the CRISPR genome editor, is thrilled with this prediction. “The less expensive it is [sequencing] gets it, this type of research is more accessible to more labs and more people, ”he says.
But computational biologist Lior Pachter of the California Institute of Technology has reservations about the new technology. He and A. Sina Booeshaghi, a graduate student, studied one of the most active genes in Levin’s blood cell group, a potential biomarker of cancer that is also known to produce a protein that athletes sometimes inject to improve their performance illegally. The latest technology sometimes lost the active gene, Pachter says. “The error rate was very high and the performance was very poor.”
The gene has a space where the same base is repeated eight times, and Ultima admits that long repetitions can weaken the accuracy of the readings. Looking elsewhere in the final sequence, Pachter found the flaws when only one base was repeated three times. He points out that a human genome contains at least 1.4 million so-called homopolymers. However, it says, “For some applications, you don’t need a perfect sequence.”
Pachter and others are also questioning the cost of $ 100. This figure only includes reagents, not labor, pre- and post-sequencing steps, and initial machine costs, the price of which has not been released. Although the actual figure is $ 100, it may not be the only one: other companies also promise $ 100 per human genome.
One is MGI, a subsidiary of China’s huge BGI sequencing company. MGI’s technology is similar to that of Illumina, but it increases accuracy by adding four bases simultaneously while sequencing DNA. It uses antibodies to keep the base from entering, which are brighter and cheaper than fluorescent dyes. Illumina also promises lower costs, and introduced new chemicals at the meeting to increase accuracy and flexibility.
To achieve this cheap rate, Ultimak and MGI both have to fill their sequencers with hundreds of genomes. But high-performance sequencing “isn’t always good for clinical practice, even in good economics,” says Greg Elgar, a genome biologist at Genomics England, because sometimes a doctor needs to examine one or a few genomes of a person. Other companies with flow cells and new chemicals can economically sequence small numbers of genomes. At last week’s meeting, Molly He, CEO of Element Biosciences, announced that the company is sending desktop sequencers that can sequence three human genomes at a time, each at a cost of $ 560. Another company, Singular Genomics, also promises benchtop technology that doesn’t require much cost savings.
These machines, like those of Illumina, MGI, and Ultima, decipher short pieces of DNA. But over the past 7 years, the two companies, Pacific Biosciences and Oxford Nanopore Technologies, have been sequencing “long readings,” thousands of bases long, which leaves fewer partial sequences to wrap up in an entire genome. The technologies “can sequence the local DNA molecule in all its luster,” says Elgar. They have struggled with low accuracy and high cost, but he says they are on their way to becoming practical tools.
Don’t count on the giant Illumina sequencer yet. Its scientists have “probably kept a couple of cards in their back pockets” to maintain their strong position in the market, says Albert Vilella, a bioinformatics and genomics consultant in Cambridge, England. However, Illumina faces unprecedented competition, he added. “It simply came to our notice then [DNA sequencing] the landscape with new eyes. ‘