29 July 2015

Cloud computing for biomedicine

Russian scientists have made an important step in the development of medicine of the future

With its help, it will be possible to search for new biomarkers of diseases associated with breakdowns in the genome and transcriptome, develop new targeted methods of cancer treatment, and search for new drugs. A number of pilot projects for testing the platform have already been successfully completed in Russia. Now the company is preparing to introduce the technology in one of the well-known Israeli clinics.

Medicine of the futurePersonalized medicine or, as it is also called, the medicine of the future is one of the most modern trends in medicine, which began to develop quite recently.

This direction should change the principles of prevention, diagnosis and treatment of many diseases, including the most severe ones, as well as the ways of developing and methods of using medicines, make this process more successful and effective.

The main idea of personalized medicine is to tell about the risks of certain diseases based on the genetic data of a particular person and make a plan for monitoring his health to prevent their development. And, if the disease has already been diagnosed, then personalized medicine will help to find out which treatment will be more effective, and which medications and in what doses will have the best result.

Genetics and biology....The emergence of personalized medicine became possible thanks to the famous human genome sequencing project – the Human Genome Project (cost $ 2.7 billion).

The project lasted 20 years from 1984 to 2003, and many research teams from all over the world participated in it. As a result, scientists have found out that the human genome consists of more than 3 billion pairs of nucleotides.

But sequencing the human genome is just a reproduction of a sequence of letters in a text that we can't read yet. Deciphering this text and understanding how the genome works is probably one of the most important tasks in biology right now, without solving which it is impossible to develop personalized medicine.

And quite a lot has already been done in this area. For example, scientists have already realized that there are structural differences in the genome. It turned out that many DNA sites differ from one person to another. The most common difference is the replacement of one nucleotide (the brick from which DNA is built) with another. The study of these differences is very important for the search for genetic variations associated with any diseases.

Biologists have also come to understand that there are also functional differences in the genome of different people related to how these genes work (transcribed). And the peculiarities of their work may also be associated with certain diseases.

Currently, systems biology has begun to actively develop, which studies the work of cellular systems as a whole: that is, it considers the interaction of DNA (genomics), RNA (transcriptomics) and proteins (proteomics).

Obviously, in any given field, scientists have to deal with a huge amount of data. For example, only the genome data of one person that came off the sequencer digitally occupies 0.5 terabytes, and this data is already three to four times more in processed form. Specialists often have to deal with the genomes of thousands and tens of thousands of people. For example, in the UK, the Genomics England project is being conducted to sequence 100,000 genomes characterizing rare and oncological diseases. The US administration has plans to sequence a million genomes, China has a plan to sequence the genomes of a million citizens of this country.

If we talk about systems biology, then the amount of data that we have to operate with is even greater. And for research in the field of personalized medicine, moreover, it is often necessary to combine data of different formats: genetic and clinical.

Obviously, processing, storing and transmitting all these huge amounts of information or "big data" is a very difficult task.

New platformThe Moscow EMC Center has developed a platform that allows you to solve this problem.

According to Kamil Isaev, Vice President of the EMC Corporation, CEO of the EMC Research and Development Center for Cloud Computing and Big Data, the main goal they are striving for is to use the platform at the sites of clinics and research and medical centers that are engaged in developments in the field of personalized medicine. Now, for example, a project is being prepared to launch to implement the platform in one of the leading Israeli clinics.

This is the largest center in the world, which deals not only with the treatment of oncological diseases, but also with scientific developments in the field of personalized medicine, including with the help of bioinformatics.

"There are hundreds, if not thousands, of mutations that lead to certain oncological diseases, but the search for protoncogens that cause cancer by mutating continues. This is the main task facing the bioinformatics laboratories of leading clinics, and they expect our help in this," says Kamil Isaev.

According to him, the introduction of the platform on the sites of clinics will give a lot. This includes the development of targeted therapy in oncology (when a drug is directed at a specific target), the selection and selection of medications, including, perhaps, those already used to treat other diseases, and the diagnosis and prevention of these diseases.

Meanwhile, several teams of Russian researchers have already used the platform developed by the Moscow EMC Center for their research in pilot projects.

"Transcriptomic data are hot cakes that are being snapped up quickly now""The basic dogma of molecular biology is that DNA makes RNA, RNA makes protein.

It is important to analyze all three components – DNA, RNA, proteins – in order to understand how the cell works. This is what systems biology does. We learned how to reconstruct genomic DNA well from short fragments, but the transcriptome required special attention. A new algorithm was needed for its assembly and analysis. Then we created an RNA data collector and connected it with a large proteomic program created by colleagues from California, on the EMC platform. As a result, this makes it possible to collect huge transcriptome data and analyze them together with proteomic ones," says Alla Lapidus, Deputy Director of the Laboratory of Algorithmic Biology at the Academic University of the Russian Academy of Sciences.

According to her, these data are very important for medicine, since transcriptome changes indicate a number of diseases, primarily neurological and oncological. "By understanding what is broken in the transcriptome, we can understand how to treat a particular disease. Transcriptomic data are hot cakes that are being quickly snapped up," adds Alla Lapidus..

From science to real medicineAnother project carried out with the help of the EMC platform has already been successfully implemented in clinical practice.

The Parseq Lab (St. Petersburg) has created a solution for the diagnosis of severe hereditary diseases in newborns - cystic fibrosis, phenylketonuria and galactosemia using genome sequencing technology. Such neonatal screening (in addition to these three diseases, it includes two more) has been carried out in St. Petersburg since the end of 2014 and is now mandatory. Moreover, this is the first case in Russia of the introduction of high-performance genomic research into ordinary medical practice.

"There is a long distance from science to real medicine. Our main goal is to introduce diagnostic tools that are created by hard work in scientific laboratories into clinical practice. Our test has been created for three diseases, on the basis of which a genetic diagnosis can be made, and already on its basis, in some cases, a clinical diagnosis can be made. This process is called translation. For some diseases, such a broadcast is a fairly simple process, for others it is an art," says Alexander Pavlov, CEO of Parseq Lab.

According to him, the main difficulties encountered in their work with genomic data are the storage, management and transmission of information. "And the EMC platform successfully solves these challenges," Alexander Pavlov notes.

Another project, also carried out on the basis of the EMC platform at the F.G. Dobrzhansky Center for Genomic Bioinformatics (St. Petersburg State University), is related to the study of the genetic diversity of the causative agent of tuberculosis. "As a pilot experiment, we assembled the genome of Mycobacterium tuberculosis (the causative agent of tuberculosis). The problem with the incidence of tuberculosis in Russia is serious. The aim of our projects is to link the genetic diversity of Mycobacterium tuberculosis strains with geographical location. This allows us to draw conclusions about the spread of strains, genetic factors that affect their sensitivity or resistance to various drugs," says Anton Svitin, a leading researcher at the Center.

Save rare animalsAnother group of projects based on the EMC platform, carried out at the Center for Genomic Bioinformatics of St. Petersburg State University, is already connected with a completely different direction – comparative and evolutionary genomics.

"We receive data on sequencing the genome of rare mammals that are on the verge of extinction, annotate this data, find out which fragments are responsible for what, what their role is. So, we have assembled the genome of the Amur leopard (Panthera pardus orientalis). There are only 50-70 of these animals left, the species is on the verge of destruction. Studying the genome of the Amur leopard, which is an endangered species, can help formulate an environmental strategy aimed at preserving this animal species. For example, if it turns out that another closely related subspecies of leopard is genetically close to the Amur, this related species can become a resource for restoring the population (for example, it was in the case of the Amur and Transcaucasian tigers). In addition, analysis of the Amur leopard genome can help assess the state of the population of this species, which is also important for conservation efforts," says Anton Svitin.

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