Genomics and Bioinformatics in Russia

Genetics

Main article: Genetics

Bioinformatics (main trends)

Main article: BioIT - Bioinformatics (main trends)

Bioinformatics (profession)

2021: Bioinformatics is becoming a highly sought-after profession

The profession of "bioinformatics" appeared not so long ago, but is already rapidly conquering the labor market. Already in December 2021, bioinformatics, working on several projects, may well receive about 500 thousand rubles a month. At the same time, they do not risk their lives or their own capital, do not really worry about their "communicative talents," even they do not always leave the house.

Previously, bioinformatics was only a subsection of Computational biology. It was considered as one of the methods of biology, and not as a huge independent direction. Probably, it is in this outdated view that lies the reason that bioinformatics is usually not listed in a number of professions of the future.

The most important discoveries are most often made precisely when scientists manage to overcome the lopsided views of each individual science and be able to look at the problem as a whole. By attracting specialists with different educations to the project and seriously considering alternative points of view, sometimes it turns out to solve even those problems that previously seemed unsolvable in a non-standard way.

So it happened with bioinformatics - a specialty somewhere in between biology, chemistry, information technology, programming, biomedicine, cybernetics and mathematics. It turns out that one criterion by which it is customary to classify professions as professions of the future has been fulfilled is multidisciplinary.

The second traditional criterion of the profession of the future is an assessment judgment, predicting its appearance only after 15-20 years. The theory is that the professions of the future will complement or replace existing ones. The most common example: truck drivers will be replaced by self-driving vehicles. At the same time, the profession of a truck driver will gradually disappear, but the profession of a drone designer will appear. Even from this example, we can understand that in fact we are more likely to talk about the scale, since drones are being designed today, the number of such specialists will simply grow significantly.

Bioinformatics is a creative profession, it is akin to art. Bioinformatics is constantly evolving. It is impossible to just learn a certain number of algorithms, learn how to analyze several types of data in general terms and expect that you will be a popular specialist for at least 5 years. Every year we see huge jumps in the level of laboratory technology, which allows us to obtain the so-called omix data in a rapidly increasing volume. More and more capacities are required to produce calculations and more and more analysis methods. Everything that can be automated without compromising the quality of the result is immediately automated. That is, in 15-20 years, the functionality of bioinformatics will be completely different; we can safely say that the second criterion of attribution to the professions of the future is also fulfilled.

What does a bioinformatist usually do at work? There can be a lot of options. The main thing that is important to know: there is practically no place for ready-made solutions - it is impossible to write an algorithm of actions once and then constantly use it. This happens because, firstly, new methods of analysis appear - and they must be included in their work, and secondly, biological processes are extremely complex: faced with the next mystery of nature, you have to solve a lot of problems in manual mode.

Bioinformatics collect the genomes of living organisms, analyze the mechanisms of how genetic information is implemented into specific phenotypic signs of organisms, study the development processes from zygote to adult organism, and study aging.

In addition to normal processes, of course, pathological ones are also being studied. Each disease has its own characteristic molecular genetic mechanisms of occurrence and progression; by investigating them, treatments can also be found. Various scientific and practical problems are investigated: the origin of life on Earth and the systematics of living things, disorders in the body of astronauts, issues of antibiotic resistance of bacteria, mechanisms of interaction of organisms in ecosystems, molecular evolution in the "parasite-host" system and much, much more.

As a rule, bioinformatics use data obtained using high-performance sequencing (NGS - next generation sequencing), use methods of working with Big Data, connect machine learning and artificial intelligence. In this profession, everyone will be able to find something special and precisely for themselves.

Bioinformatics is becoming an extremely popular profession: the industry is good, it is financed states it is actively developed by universities and companies. For applicants, this is a promising direction: it makes it possible to get an interesting job with decent earnings^[1]

2015: How to become a bioinformatic

Bioinformatics are needed by companies that are engaged in drug development and personalized medicine. Typical tasks for such a specialist are the development and analysis of databases, the search for targets for molecules and new regulatory pathways, the identification and annotation of mutations, statistical analysis.

Among the current vacancies are positions of researchers, technologists and analysts, as well as management and management positions for graduates of universities and educational programs in the specialty "bioinformatics."

For 2015, bioinformatics can be studied at Moscow State University, HSE, MIPT, Skolkovo Institute of Science and Technology and other Russian institutes at medical and biological faculties, as well as at the faculties of applied or computational mathematics and cybernetics.

Higher education can be obtained at the following universities:

• Faculty of Bioengineering and Bioinformatics, Moscow State University.
• Master's degree"Data analysis in biology and medicine" at the Higher School of Economics, Moscow
• Department of Bioinformatics, Faculty of Biological and Medical Physics, MIPT, Moscow
• Master's program "Biomedical Sciences and Technologies," Skolkovo Institute of Science and Technologies, Moscow. Studies partially take place abroad.
• Department of Bioinformatics, Faculty of Medicine and Biology, Pirogov Russian National Research Medical University, Moscow
• Department of Mathematical and Information Technology, SPbAU RAS St. Petersburg
• Department of Applied Mathematics, Institute of Applied Mathematics and Mechanics, SPBPU
• Department of Bioinformatics, Faculty of Computational Mathematics and Cybernetics, NNSU, Nizhny Novgorod
• Department of Bioinformatics and Medical Cybernetics, Institute of Fundamental Medicine and Biology, KFU, Kazan
• Department of Bioengineering and Bioinformatics, Institute of Priority Technologies, VolSU, Volgograd
• Specialty of Bioengineering and Bioinformatics, Faculty of Biology, SSU, Saratov
• Department of Information Biology, Faculty of Natural Sciences, NSU Novosibirsk

The number of programs in the field of basic and additional education is growing:

• new master's programs are opening (for example, a master's degree in FIZTECH), training centers (School of Bioinformatics, Moscow;
• Institute of Bioinformatics, St. Petersburg),
• short-term courses and schools in bioinformatics (Blastima Training Center, Moscow;
• Events of the Institute of Bioinformatics, St. Petersburg and Moscow;
• NGS electives at Moscow State University, Moscow;
• CSHL Summer Schools, Moscow;
• School of Bioinformatics within the framework of the conference "Genomic Sequencing," Moscow;
• School at the conference "Molecular Phylogenetics," Moscow),
• online courses in Russian and English and training programs (Introduction to Bioinformatics, Bioinformatics Algorithms, Bioinformatic Methods I, Bioinformatic Methods II, Bioinformatics: Life Sciences on Your Computer, Introduction to Biology, Data Toolbox Rosalind).
• There are special events, Summer Schools of Bioinformatics, seminars that allow you to popularize bioinformatics and spread knowledge about it. Among them is the first hackathon in bioinformatics, which took place in the spring of 2015.

Biohacking

Main article: Biohacking

Genetic passports

Main article: Genetic passports

Genomics and Agriculture

The main direction is to obtain animal breeds and plant varieties with economically valuable properties. Now the methods of classical selection are fading into the background. Accelerated selection by genetic traits is increasingly entering practice. How is this done? At the first stage, genomic sequencing is carried out, that is, decoding of the DNA sequence, for a large number of organisms with the widest possible range of features. Then these huge amounts of data fall into the hands of bioinformatics, they look for associations between genome features and specific phenotypic traits, for example, the plant's resistance to pathogens or low temperatures. As a result, scientific breeders receive information about marker points, on the basis of which they effectively select pairs for further crossing and breeding^[2].

Genomics and Ecology

To monitor the state of the environment and protect it, the most effective method of genomics is dynamic analysis of the composition of the microbiota in various habitats. Usually, the analysis takes into account bacteria, fungi and archaea, forming together the so-called consortium of microorganisms. An alternative design of experiments can be used for each particular task, but all of them are ultimately reduced to a list of microorganisms (a level of a species or group of a higher rank). The proportion in the community for each taxon is specified, and quantitative indicators of the representation of each taxon in the absolute scale can also be given. For analysis, high-performance genomic sequencers are used - devices that allow you to receive relatively long and high-quality "readings." DNA decoding takes place in the mode of paired-end "readings," each of which consists of 150-300 nucleotides.

Research on microorganism consortia plays a crucial role in the development of biological methods of cleaning the environment of biogenic pollution, that is, those that occurred as a result of human activity. A special role is given to the use of microorganisms for wastewater treatment at special treatment plants. The composition of wastewater can vary greatly. Moreover, in order to obtain compounds that are safe for nature from dangerous components, various types of microorganisms are often required. By the qualitative and quantitative composition of the consortium, it is possible to predict, firstly, which pollutants (xenobiotics) can process the treatment facility under study, and which cannot, and secondly, it is possible to predict how many days the wastewater of a certain composition must be in the treatment zone in order to fully comply with sanitary standards.

A very similar situation is observed during bioremediation - soil restoration after pollution, mainly with dioxins. One method of purification is to create a collection of microorganisms that specifically degrade typical contaminants. Further, biomass is obtained on an industrial scale and then introduced into contaminated areas. The method is very promising, but there are also methodological difficulties that have not yet been overcome. The main problem is well known to everyone - even the most useful strains of microorganisms, but strangers to our individual intestinal consortium of microorganisms, do not take root in it. Beginners do not become native to the community, soon they are completely replaced by natural microflora.

For any habitat, any biotope, regular monitoring of the composition of the community of microorganisms can be carried out. High-throughput sequencing of samples for the analysis of the metagenome (a collection of genetic material of microorganisms) allows monitoring the ecological state of the object. The fact is that a change in the chemical composition of the substrate inevitably causes changes in the bacterial composition; genomic sequencing allows the detection of changes with high accuracy.

Studying the genomes of living organisms can be a very valuable tool when trying to recreate the course of history, that is, when building a phylogenetic tree. In essence, this is a way to organize the systematics of living beings in such a way that it reflects the natural evolutionary processes of^[3] the^[4].

Biomedicine

This is now the most relevant and demanded area of ​ ​ application of genomics. The modern concept of health care postulates the need to apply the four P model (4P medicine), which integrates the concepts of personalization (individual approach to each patient), prediction (identification of predisposition to the development of the disease), preventive (prevention of the appearance of diseases), participativity (motivated participation of the patient). Advances in genomics, along with other "omix" technologies, are the basis for implementing this model. I will briefly list the main promising areas of application of genomics achievements in biomedicine. Each of them deserves a separate detailed story - read about it in our next issues. Several applications can be combined as ways to diagnose hereditary diseases, conditions and predispositions. Breakthrough results can be expected as genetic information centers are established worldwide, especially when it is possible to combine and jointly analyze data from different countries. It is critical that the genomes of people with a qualitative and detailed description of the clinical picture be included in the analysis. The analysis of the embryo genome before planting into the mother's body as part of the IVF procedure already now allows you to effectively prevent severe monogenic diseases and genetic syndromes.

The next direction follows from the previous group, it can be designated as human design and the prevention of hereditary diseases by correcting the genome. Apparently, sooner or later, humanity will consider it ethically acceptable to make changes to the genome of somatic cells and even correct the entire body, ensuring the heritability of the introduced change in a number of generations. However, scientists are almost unanimous in the opinion that the spread of such technologies will serve as a powerful trigger for strengthening social stratification and differentiation of society.

The importance of diagnosing disorders acquired by the body during development, as well as analyzing the characteristics of metabolism and signaling processes in cells, is most clearly manifested in oncology. Personalized treatment allows a significant increase in life expectancy, since drugs are prescribed depending on the test results.

The composition of the gut microbiota, formed as a "core," that is, a basic community in the first month of a child's life, can also transform under the influence of various substances. So far, genomic sequencing of fecal samples is not a medical service in the strict sense of this concept, but already now data on the analysis of metagenome are used in their work by nutritionists, proposing to adjust the diet of patients in such a way as to increase the duration of active life.

Genetic engineering

• Genetic engineering (genetic engineering)
• Genetic data banks (biobanks, biorepositories, storing biological samples)

Federal Scientific and Technical Program for the Development of Genetic Technologies (FNTP)

• Federal Scientific and Technical Program for the Development of Genetic Technologies (FNTP)

2023: Kurchatov Institute allocated 8.8 billion for the development of genetic technologies

In mid-June 2023, the Russian Government allocated 8.8 billion rubles for the development of genetic technologies. National Research Center (NRC) Kurchatov Institute. The funds will go to the development of scientific laboratories, as well as world-class genomic research centers. Read more here.

2021

Establishment of a genomic sequencing center in the Russian Federation

On November 17, 2021, Russian President Vladimir Putin announced the creation of the Center for Genetic Information on the basis of the Vavilov All-Russian Institute of Plant Genetic Resources. Read more here.

More than 10 billion rubles have been allocated for genetic research and bioresource collections

On September 20, 2021, it became known about the allocation by the Government of the Russian Federation of more than 10 billion rubles for the creation of 15 bioresource collections and 25 research programs in the field of genetic technologies in Russia. Grants will be issued on a competitive basis.

128 applications from 35 regions of 8 federal districts of the country were submitted to the competition aimed at solving major world-class applied problems and creating leading research teams in the field of genetic technologies.

The Ministry of Education and Science of Russia will allocate more than 10 billion rubles for the development of genetic technologies

Support for the development of bioresource collections is implemented on the principles of network interaction between collections of scientific and educational organizations, which in the future will be able to unite into large bioresource centers. Such support for collections throughout the country is being carried out for the first time, this will increase their availability and demand. Particular attention will be paid to research programs aimed at ensuring global leadership and solving fundamentally new world-class tasks, - said the Minister of Science and Higher Education Valery Falkov, whose words are quoted by the press service of the department, which he leads.

By September 2021, three genomic research centers are operating in Russia. They function in four areas: biological safety and ensuring technological independence, genetic technologies for the development of medicine, agriculture and microbiology.

This was reported at a meeting of the Council for the Implementation of the Federal Scientific and Technical Program for the Development of Genetic Technologies for 2019-2027. The preliminary results of the activities of genomic centers were also considered there. During the work of the organizations, specialists deciphered the genomes of agricultural crops, tested enzymes against Staphylococcus aureus, developed digital passports of 1,500 strains of microorganisms, and also created a prototype of a technological treatment for Duchenne myodystrophy.^[5]

11 billion rubles allocated for the development of genetic technologies in Russia

More than 11 billion rubles have been allocated for the development of genetic technologies in Russia. Deputy Prime Minister Tatyana Golikova announced this on April 14, 2021.

According to her, most of the funds (734 million rubles) for the implementation of the program for the development of genetic technologies in Russia will be from extrabudgetary sources.

The program has identified four areas of implementation based on the development of genetic technologies, these are biosecurity and ensuring technological independence, genetic technologies for the development of agriculture, genetic technologies for medicine, genetic technologies for industrial microbiology, the Deputy Prime Minister quoted Interfax as saying these words at the Council for the Implementation of the Federal Scientific and Technical Program for the Development of Genetic Technologies for 2019-2027.

11 billion rubles allocated for genetic technologies in Russia

Golikova added that the total amount of financial support in accordance with the plan for the implementation of the program for a three-year period in 2020 amounted to 11.6 billion rubles, of which 432 million rubles were raised from extrabudgetary sources.

As an example of developments in 2020, the Deputy Prime Minister named for the first time developed in Russia at the Center for High-Precision Editing and Genetic Technologies for Biomedicine Technologies for the Treatment of a Group of Neuromuscular Diseases, a therapeutic approach to the treatment of Duchenne Myodystrophy (muscle weakness, difficulties with movements since childhood, which progress over time).

The creation of at least three genomic research centers is provided for by the Nauka national project, which should be implemented in Russia by 2024. In total, it is planned to allocate more than 625 billion rubles for its implementation. It also involves the creation of 15 world-class scientific and educational centers in the country, the commissioning of scientific installations of the "megasayence" class and the formation of an integral system for training scientific and scientific and pedagogical personnel.^[6]

Genetic technologies in industry

2024: A test system has been released in Russia to identify 2.5 thousand hereditary diseases in newborns

On February 20, 2024, Prime Minister RFMikhail Mishustin announced the release in Russia of a new test system for determining inherited diseases in newborns. Read more here.

2022: Putin instructed to create a mechanism for the introduction of genetic technologies in industry

At the end of January 2022, the President Russia Vladimir Putin instructed Government of the Russian Federation to create a mechanism for the prompt introduction into industrial production of applied results of activities in the field of genetic technologies.

To ensure the creation of a mechanism for the prompt introduction into industrial production of applied results of activities in the field of genetic technologies, including through the involvement of industrial (technological) partners in the early stages of research and development, including preclinical research of medicines, - says the list of instructions following the meeting on the development of genetic technologies (quoted by the Kremlin press service).

Vladimir Putin instructed to create a mechanism for the introduction of genetic technologies in industry

Putin instructed to involve industrial and technological partners in the creation of the mechanism in the early stages of research and development, including preclinical drug research. Measures to accelerate the registration of innovative drugs must be worked out with the member countries of the Eurasian Economic Union (EAEU).

In addition, it was instructed to ensure the synchronization of state support measures provided to developers and manufacturers of domestic equipment that allows for world-class research in the field of genetic technologies and consumables for it, as well as improving the mechanisms of state support for such manufacturers.

The report on behalf of is established by September 1, 2022 and further - annually. Mikhail Mishustin Tatyana Golikova The Prime Minister of the Russian Federation, Deputy Prime Minister and Presidential Aide were appointed responsible for its execution. Andrey Fursenko

Vladimir Putin also instructed to ensure the introduction of amendments to the legislation aimed at extending until 2030 the period for the implementation of the federal scientific and technical program for the development of genetic technologies for 2019-2027, and to clarify the target indicators, indicators and the amount of resource support for measures within the framework of such a program.^[7]

Diagnosis of genetic diseases

Genomics and Bioinformatics Market

2022: Data on decoding the genome of pathogens of infections will be entered into the Sanitary Shield IT system

In December 2022, Prime Minister Mikhail Mishustin signed a decree "On Amending the Appendix to the Regulation on the Federal State Information System of Sanitary and Epidemiological Information." According to the document, data on decoding the genome of pathogens of infectious and parasitic diseases will be entered into this system. Read more here.

2021: A platform for joint work of genetics and biotechnology specialists has been launched in Russia

At the end of November 2021, it became known about the launch of the BioTools4You platform developed by BioTulaFU, designed to unite the creators of tools for analyzing genetic data, interpretation, owners of genetic data, as well as geneticists and laboratory geneticists. Read more here.

2015: Shaping the Market

In 2015, the Russian market for genomics and bioinformatics continues to be actively formed. The main scientific centers at this time are still Moscow and St. Petersburg.

Bioclusters (Severny biopharmkslaster based on MIPT) are being created, as well as special workspaces for the work and development of knowledge-intensive projects (Biokluk), uniting specialists from the field of bioinformatics, commercial companies and representatives of the scientific environment. In the future, on their basis, it is planned to organize large bioinformatics festivals, including hackathons, various courses, intensives and lectures.

The development of such an event infrastructure and the gradual "opening" of the market are increasingly attracting the attention and interest of investors: representatives of funds can more often be found at specialized events.

A number of scientists and bioinformatics specialists are returning from abroad back to Russia, having studied there, or having gained experience in scientific activity, because they see that the Russian bioinformatics market is developing, including starting to attract funding, which is important for young scientists and graduates of universities. And this trend certainly has a positive effect on the overall state of the market.

Although positive dynamics are noticeable, weak government support remains important restraints to the holistic development of the bioinformatics market; the distrust of physicians and patients of the principles of personalized medicine and, in general, the possibility that such a transition will occur and new medicine will work effectively; weak public awareness of the possibilities of modern genomics.

In addition, bioengineering, which supports bioinformatics' from below ', providing it with material (reagents, biomaterials, etc.) for further analysis and research, is now in a very difficult situation. Delivery of reagents from abroad is difficult and can last months due to long delays at customs. These conditions, respectively, negatively affect the development of bioinformatics in general.

Many major universities in the country still lack specialized courses in sequencing technologies (DNA decoding), working with data obtained from sequencing, their analysis and application in bioinformatics. However, the situation is changing, universities are beginning to turn to the leading specialists in the market, to create opportunities for additional education within the framework of existing educational programs.

Notes