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The million genome problem

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The million genome problem

A few days ago, we celebrated the 70th anniversary of Jim Watson and Francis Crick’s landmark publication in the journal Nature of the work on the structure of DNA that has changed our understanding of life and medicine.

This discovery deservedly received the Nobel Prize in 1962. Unfortunately, Rosalind Franklin, who made a significant contribution to this discovery, was not fortunate enough to be included in the choir of Nobel laureates, since she died in 1958 at the young age of 38 from ovarian disease. cancer. In the 70 years since this discovery, progress has been incredible in both biology and medicine.

My purpose here is not to enumerate the benefits that the discovery of the structure of DNA has brought, but to discuss a practical problem that is of concern to the world scientific community and the solution of which will give new impetus to international medical practice.

The genome of each person (that is, the totality of DNA) is a vast but finite text of biological information that exists in the nucleus of each cell. The size of the genome, written with only 4 letters (chemical stones) A, C, G, T, is approximately 6 billion letters, half from the father and half from the mother. The genome of each person is diverse, that is, it has small differences (about 0.9%) from person to person, so that each person is different from all other people. This diversity is a great gift of nature, because it allows us to adapt to an ever-changing environment and develop further. But sometimes this diversity is pathological and causes genetic diseases or a predisposition to many diseases in adulthood.

Thus, the main question of the last 20 years (which will also be the question of the next 20-30 years): what kind of DNA diversity is “normal” and what is pathological.

Answering this question is sometimes easy, and sometimes very difficult, because most of the genome is functionally unknown. Reading the genome of each person reveals millions of variations that differ from the reference genome, as we say, that is, the genome that exists in international databases and is, by conventional wisdom, a common point of comparison. So what is the smart thing to do? Read the genomes of millions of people from all latitudes and longitudes of the planet, in people of all geo-ethnic groups, of all ages, from all diseases. Ideally, one could imagine reading the genomes of all people on earth and comparing them to the diseases of each/all. You understand that this is now impossible because of the cost, the acceptance of the idea and the impossibility of registering phenotypes, which in the language of medical biology means all the features and diseases of each person.

So a few years ago, the reading of the genomes of a number of people began timidly. How much so far? It is difficult to collect data from all over the world. I would say about 2 million. This number seems large at first glance. In reality, however, it is quite small and tens or hundreds of millions of read genomes and their correlation with thousands of diseases (including hundreds of cancers) are needed to draw causal conclusions, i.e. what diversity of the genome causes a particular disease. . this disease.

In addition, the vast majority of genomes read so far are from people of European ancestry. This, on the one hand, limits the recognized diversity to one part of the world, on the other hand, does not cause social inequality in ensuring the health of all people. The genomic diversity of Africans is richer than that of other regions because our species first appeared in Africa and thus the inhabitants of this continent have a longer biological history and therefore greater diversity.

And then there is the political and national factor: data collections containing genomic diversity are fragmented, incomplete, inconsistent, and mostly national. In America, for example, the public database contains 132,000 genomes available to researchers. Another biogenetic company’s database contains about a million hard-to-find genomes. Another database in Boston contains 141,000 genomes from many parts of the world available to researchers. I estimate that another 500,000 or so genomes are being read in diagnostic labs and not available for data protection reasons, which I consider a theoretical problem since the datasets are catalogs of diversity rather than lists of individual genomes. Distribution of individual collections of the genome is also problematic, as it requires constant and intense review from collection to collection in order to get a clear idea of ​​the nature, frequency, and impact of each variation.

A few years ago, I proposed a simple solution to the problem in Science magazine. All read genomes are stored in a data collection accepted by all research institutions: the World Health Organization.

WHO has the potential to develop such activities, and with prestige and political recognition from all health systems, it could promote genomic research. The cost of such a single collective database could be covered by the amount of research currently consumed by each country individually, and economies of scale would reduce costs. In addition, the bioethical constitution and the international attention of the WHO will guarantee that any deviation from the scientific and medical goal of the project will be prevented. Initially, this proposal was well received by the US National Institutes of Health, and also showed interest from the WHO, but other priorities, mainly infectious diseases and the absence of an appropriate genetics department in the WHO, delayed discussion of this international problem. In this regard, I would like to draw the attention of the responsible Greek Ambassador to international organizations to put this proposal on the WHO agenda on his own initiative.

Understanding the meaning of genome variation is a matter of better life, longer life, fewer diseases, earlier prediction and targeted therapy! Every effort in this direction is a step towards a healthier society. Every time we clink glasses in “our health”, we think about the genome. This is the only long-term benefit that we give to future generations.

* Stylianos Antonarakis is Professor Emeritus of Genetic Medicine at the University of Geneva, Member of the Swiss Academy of Sciences and former President of the International Human Genome Organization (HUGO).

Author: Stylianos Antonarakis

Source: Kathimerini

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