Genome for $100
American startup promises to sequence genome for $100
Irina Konova, PCR.news
According to the Ultima Genomics Delivers the $100 Genome press release, the new platform for massive parallel synthesis sequencing, designated UG 100, includes the sequencer itself and data processing software. A number of solutions can reduce the cost of sequencing to $1 per gigabyte. So, the technology eliminates the flow cell. Instead, a silicon substrate is used. It is marked with areas with which DNA binds due to electrostatic forces. The company's specialists claim that both the substrate and its processing method are widely used in the semiconductor industry and are inexpensive.
When preparing DNA, clonal amplification is used on beads, each of which is located in a drop of water in an emulsion system. The surface area of the substrate allows you to place more than 10 billion on it. beads. According to the developers, there is a groundwork for further increasing their number.
For sequencing, mainly unmodified nucleotides are used that do not interrupt the reaction. Less than 20% of nucleotides carry a fluorescent label. As a result, unmodified DNA is synthesized. The growth of the chain is recorded by the optical system. A special system for the delivery of reagents to the substrate ensures their economical consumption. Processing of the received data is carried out using a neural network trained on terabases of sequences. Ultima Genomics claims that the maximum length of the reed obtained with the UG 100 exceeded 400 bp.
Several research centers have received the UG 100 platform under the early access program and are ready to share the results. For example, the Brod Institute (USA) used a new platform to sequence more than 200 human genomes. The results are posted on bioRxiv. First, scientists sequenced seven standard "genomes in a Bottle" (Genome in a Bottle, GIAB), HG001–HG007. The average length of the rids was 282 bp, the average coverage per sample was 60X, more than 99.9% of the rids were mapped to the reference human genome GRCh38. At the next stage, UG 100 was used to sequence 224 samples from the 1000 Genomes project. The average coverage was 56X per sample, the average reed length was 279 p.o. When processing the data, the scientists noted errors in the recognition of variants that can be solved by optimizing the clonal amplification protocol.
Another preprint with the UG 100 test results was posted to the bioRxiv database by the Stanford University team (USA). The scientists used the platform to analyze the change in methylation patterns associated with the transformation of precancerous polyps into colorectal adenocarcinoma. At the first stage, the scientists compared genome-wide methylation data for standard references HG001, HG002 and HG005 obtained on UG 100 and other methods, using the results as a reference EpiQC. They noted the consistency of data from UG 100 and other platforms and high coverage. Then UG 100 was applied to blood samples and freshly burned samples of normal intestinal mucosa, polyps and cancer from nine patients with familial adenomatous polyposis. Scientists have discovered tens of thousands of sites of differential methylation, confirmed that a gradual change in the nature of methylation is associated with the development of cancer, and described specific patterns for genes and regulatory regions. Despite the fact that for final conclusions it is necessary to analyze a larger number of samples using the new platform, the authors hope that the data sets obtained will serve as a valuable resource for further research.
The work of a team from the Whitehead Institute on the use of UG 100 for the analysis of single cells is also being prepared for publication. All users of the new platform will talk about it at the conference "Advances in Genomic Biology and Technology", which will be held from June 6 to 9 in Florida. Scientists are already calling the UG 100 architecture revolutionary, overcoming the limitations of traditional NGS technologies.
Illumina was the first company to announce its intention to sequence the human genome for $100 in 2017. In 2020, the same plans were announced by the Chinese firm MGI. However, no one has managed to achieve this goal so far. Today, the cost of one genome has fallen below $1,000, but for several years it has been at the level of $6-10 per gigabyte.
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