The end of the beginning of genome decoding

Yana Khlyustova, "Newspaper.Ru" 

The key to the treatment of cancer, blood clotting, Alzheimer's disease and many other diseases was obtained during a large-scale seven-year project to decode the human genome, which ended on Thursday night. As a result, geneticists have completely deciphered the genomes of more than 2.5 thousand people, each of which consists of 3 billion genes. The scientists told the science department of the Newspaper about their work and plans.Ru».

1000 Genomes Project is a large–scale project launched in January 2008, the initial goal of which was the complete sequencing (decoding) of the genomes of thousands of people – representatives of different races and nationalities. Teams of researchers from the USA, Great Britain, Italy, Peru, Kenya, Nigeria, China and Japan took part in the work. Decoding the complete human genome is not an easy task, since it contains 20-25 thousand active genes. However, this makes up a very small part of all genes – the rest belong to the so-called "junk DNA", that is, they do not encode any proteins. But taking into account the "junk DNA", the volume of the human genome reaches about 3 billion pairs of nucleotides.

The large-scale work done by scientists is directly related to all people living on the planet. During the work, scientists managed to decipher the genomes of 2504 people representing 26 different populations. Researchers have been able to determine exactly what variations each human gene has – and this may help in understanding which genetic disease it is responsible for. Scientists have already managed to understand which genetic variations are responsible for the occurrence of diseases of the heart muscle (myocardium), chronic inflammation of the gastrointestinal tract, sickle cell anemia (hemoglobin disorders) or Gaucher disease - a hereditary disease that leads to the accumulation of complex fats in many tissues, including the spleen, liver, kidneys, lungs, brain brain and bone marrow.

The data obtained as a result of the work is available on the website of the project itself. On the night of Tuesday to Wednesday, two articles were published in the journal Nature, presenting the latest overview data that were obtained during the work: An integrated map of structural variation in 2,504 human genomes and A global reference for human genetic variation. 

To the correspondent of the science department of "Gazeta.Ru" managed to communicate with three scientists who were directly involved in the decoding of the human genome: Paul Flicek (one of the leading researchers of the 1000 Genomes Project and a leading researcher at the European Molecular Physics Laboratory), Gonzalo Abecasis (professor at the University of Michigan) and Adam Othon (Albert Einstein New York Medical College) and to talk with them about future plans and the possibility of practical application of the results of seven years of work.

– In 2008, when the project was just beginning, scientists had a goal: to decipher the complete genome of thousands of people. In October 2012, the journal Nature announced that the decoding of 1092 genomes had been completed. At the moment – by the end of the project – you have managed to sequence 2504 genomes. Tell me, how did you manage to exceed the plan so significantly?

Paul Flichek: We were able to sequence so many samples because in recent years, the technologies that allow genome sequencing have developed significantly. That is why we managed to get about 25 times more data than was originally announced.

Gonzalo Abecasis: Do not forget about the cost of such an analysis. If in 2008 the complete decoding of the human genome cost about $ 100 thousand, now this amount is less than $ 2 thousand.

– On September 30, it was announced that the final stage of the project was completed. Is it possible to talk about the complete completion of the work, or are you going to go further and set new goals for yourself?

Paul Flicek: We are facing a lot of new goals concerning both DNA sequencing and the search for relationships between variations of different genes, the occurrence of genetic diseases and other human characteristics. The completion of the 1000 Genomes Project is really the culmination of the efforts that we started 15 years ago and whose goal was to create an open resource containing information about human genes.

In the future, we plan to expand the base of our research and involve people representing a larger number of populations from around the world – there are populations in Africa, Asia and the Middle East that are not involved in the study. Now this work will be carried out within the framework of the International Genome Sample Resource project.

Gonzalo Abecasis: In addition, in the future we plan to focus on how variations of each gene affect the course of a particular disease. To do this, you need to study as many cases of the course and treatment of such diseases as possible.

Adam Othon: And we're also going to test how genetic variations affect a person's phenotype.

– Is it possible to apply the information you have received in practice already now? Or does it still take extra time to process the data?

Gonzalo Abecasis: The information we have collected is useful for researchers right now – it helps scientists understand how many variations each gene has, which of these variations are responsible for the occurrence of different diseases. However, it will take some time before this knowledge leads to the development of new drugs.

Adam Othon: The information is actively used, and not only by doctors, but by everyone in general. If a researcher – from any field – wants to find out what functions a gene performs, how it is distributed among the population of the globe or what some part of the genome looks like, he can easily get this information.

Paul Flichek: I think the main practical benefit of the data we have obtained is that they help to map the spread of a gene on the planet. Let's say a person from Asia was found to have a rare genetic disease. But the data of our project says that a variation of some gene (causing this disease) is only in the DNA of Africans. This will mean that the roots of the disease should be looked for in changes in another gene. In addition, we began to better understand how different populations of people migrated around the world. 

– If you were asked to describe the results of seven years of work in one or two sentences, what would you say?

Paul Flicek: The most important result of the 1000 Genomes Project is the compilation of a catalog of human gene variations and the analysis of methods and tools that can be used for further sequencing of the human genome. This catalog is completely free and is publicly available.

Gonzalo Abecasis: Now we have a catalog where different versions of each DNA sequence, and therefore each gene, are presented, and with the help of which we can determine in which regions of the planet each version is distributed. We can use this information to reduce the time and cost required to decode the genome of other people.

Adam Othon: The 1000 Genomes Project has significantly improved our understanding of how variations of human genes are distributed in the world.

– And the last question: how do you feel now that the seven-year project in which you were directly involved has been completed?

Gonzalo Abecasis: I feel that the time has come to accept the following challenge: to put what we have learned into practice and start developing methods for treating genetic diseases.

Adam Otton: The project has become the basis for further work: everyone wants to know what gene variations can tell us about various diseases. The next few years promise to be very busy.

Paul Flichek: I'm a little sad. Our project was a vivid demonstration of what modern technologies are capable of. The project was constantly growing and developing – along with the development of technology, and its completion really means the end of an era. Although, of course, the use of the data obtained during DNA decoding is just beginning, and it seems to me that the 1000 Genomes Project can be compared to a child who still has to grow and grow.

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01.10.2015