Scientists cut genome assembly time using quantum algorithms

Russian scientists have accelerated genome assembly using quantum annealing. The results of the experiment, described in Nature Scientific Reports, will speed up the process of detecting cancer cells. This was reported to “Haytek” in the press service of the Russian Quantum Center.

A group of scientists from the Russian Quantum Center under the leadership of Alexei Fedorov, together with researchers from the Genotek company, reduced the genome assembly time using quantum and quantum-inspired algorithms. During the experiment, the researchers compared the data obtained on the quantum annealing device and the Russian SimCIM software emulator for model data and for the genome of a real bacteriophage organism.

Acceleration of genome assembly in the absence of a reference one using quantum computers will make it possible to use the obtained data for the provision of emergency medical care and in the analysis of new types of diseases. Despite the fact that the complete reconstruction of the original genome, which is necessary to personalize the medical approach, is still not possible on quantum computing devices due to their insufficient power, scientists managed to develop an algorithm and solve a number of technical difficulties, thereby increasing the accuracy and speeding up the data analysis process.

Quantum computing devices are able to process more variables, while significantly reducing not only time, but also financial costs. The results can greatly facilitate the study of new types and structural changes in DNA that cannot be detected by the method of classical mapping, and genomic rearrangements in cancer cells. Thus, the introduction of quantum technologies contributes to the faster development of personalized medicine.

The first genome was sequenced more than 40 years ago (bacteriophage ФХ 174). However, if the first assembly of the human genome took about 13 years, today public and private institutions are able to implement this process in a few weeks. The participants in the experiment showed the effectiveness of quantum computing in bioinformatics problems, for the first time conducting research on the basis of both real and simulated data.

“One of the biggest challenges in quantum computing is finding useful applications. Bioinformatics and genetics often face complex computational problems that can be accelerated by quantum computers. As part of our research, we have shown the possibility of using certain types of quantum computers – quantum annealing devices – to solve genome assembly problems. We also used a quantum-inspired annealing algorithm, which is based on simulating the behavior of quantum systems. In the future, the range of application of quantum computing technologies in problems of genetics can be significantly expanded, ”said Alexey Fedorov, lead author of the study.

“The capabilities of quantum computers allow us to take a fresh look at problems, including bioinformatics, which previously seemed computationally too complex. In our study, we assessed the prospects for using quantum computers in the analysis of the genomes of humans and other organisms. At the junction of these areas, new methods appear, with the help of which growing volumes of data are analyzed more qualitatively (note, the genome of one person occupies about 100 Gb). In addition, new methods allow you not to wait for days for the results of genetic research in situations where the clock is counting ”- said Alexander Rakitko, Genotek Product Director.

ICQT is the largest Russian and one of the most prestigious world conferences on quantum technologies. The program includes not only high-level scientific reports, but also an Open Day for a wide audience. This year the conference was organized by the Russian Quantum Center, the State Atomic Energy Corporation Rosatom and the National Quantum Laboratory. The general partner of the event is Sberbank. The partners were the Russian Academy of Sciences, Gazprombank, the Roscongress Foundation and MISiS. The event takes place within the framework of the Year of Science and Technology.

The results were published in Scientific Reports and presented at the VI International Conference on Quantum Technologies ICQT-2021. The study was also supported by the Russian Science Foundation, as well as access to quantum computing devices as part of the global fight against COVID-19.

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Alexandr Ivanov earned his Licentiate Engineer in Systems and Computer Engineering from the Free International University of Moldova. Since 2013, Alexandr has been working as a freelance web programmer.
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Alexandr Ivanov

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