Using Genomics for the World of Tomorrow: This is Where We Stand… Are We Ready?

- June 29, 2017

The media more often report the challenges represented by climate change, population density, farming practices and the sustainable management of natural resources through a pessimistic—even a catastrophic—lens. Yet, Philippe Rigault, the President and founder of Gydle, maintains that human development indicators such as life expectancy, education, improvements in the status of women, the reduction of poverty and hunger, the number of war casualties, etc. are constantly improving, so that objectively speaking, “things were no better before”.

In fact, certain global problems such as acid rain, the hole in the ozone layer and population growth in developing countries were resolved in very large part when a consensus was reached as to the proper course of action to take.

Managing the planet using genomics

Philippe is one of those fundamentally optimistic scientists who are convinced that scientific and technological advancements, which require new knowledge, have allowed for human progress and that it is by continuing along the same path that the new challenges before us will be resolved. We must therefore develop a real management plan for the planet by changing our way of life, our way of farming and producing goods and our way of managing ecosystems so as to address all of the challenges before us simultaneously. This means optimizing production yields and the efficiency of sustainable farming practices, ensuring public health and protecting biodiversity while taking into consideration the new climate realities in an open world. To achieve this, we must first and foremost know about the living world around us so that we may take action to meet these challenges. This is the ambitious gamble of genomics.

Genomics is a field that combines biology, genetics and informatics to study genomes, i.e. the genetic material in the form of DNA that makes up every living being. Having knowledge of the genome makes it possible to interpret this information, viewing it as a biological recipe for life, and to understand all of the molecular data of an organism as well as their function. Such knowledge also provides insight into genetic differences between individual members of the same species which underlie genetic diseases, personalized medicine, and different forms of cancer, but also all farming practices and improvements to certain organisms using technology. Finally, since all living organisms have common ancestors, comparing genomes makes it possible to study the evolution of species as well as the mechanisms and factors that have allowed them to adapt, and to understand ecosystems and biodiversity.

Philippe Rigault founded Gydle, a Québec-based bioinformatics firm, in 2008 after acquiring 17 years of international experience mapping the human genome (Généthon) and working in biotechnology (Incyte and Illumina), as well as being involved in university and pharmaceutical research. Gydle’s mission is to develop tools to assemble, analyze and compare genomes.

The genome is a puzzle for living things that is pieced together using algorithms

Philippe explains that “assembling a genome is like putting together a puzzle with no picture to guide you. You have the pieces and can see which ones would generally go together. We use this information to put the whole puzzle together using algorithms.” Where the genome is concerned, the pieces of the puzzle are sequenced DNA fragments (a hundred or so A, C, G or T base pairs) that are compared by aligning the sequences. The solution represents the DNA of the complete genome. The smallest genomes are composed of a million base pairs (e.g. for viruses and bacteria) while those for plants and animals are gigantic (from hundreds of millions to tens of billions of base pairs), requiring combinatory analyses of billions of fragments. DNA sequencing technology has made huge strides (25 years ago, it cost a dollar to sequence one base pair whereas today it costs the same amount to sequence 10 million base pairs). In fact, since sequencing technology has evolved even more quickly than information technology, the assembly and analysis of finished genomes are now the limiting factors.

That is why Gydle has been developing high-performance technology over a number of years to assemble, compare and analyze genomes in detail. Compared to other solutions, the Gydle nuclear DNA aligner is much more efficient due to the optimized multicore processors and memory. Data stored in the Gydle (GYM) format is 50 times more compact and is fully processed in an integrated visual environment (Vision). Gydle is teaming up with leaders in the field of genomics to provide solutions for all types of genomes and applications for farming, human health, forestry, bioenergy and biodiversity. For example, Gydle technology made it possible to assemble the finished genome for the chloroplasts of forty or so species of eucalyptus, thereby mapping all of the genetic changes for this family of plant over the last 80 million years. This provides an exceptional body of knowledge making it possible to better classify these plant species, to understand how they have adapted over time and to determine changes relating to more effective photosynthesis.

After seeing bioinformatics evolve over 25 years, from the mapping of the first human genome to quick and inexpensive genome sequencing, Philippe believes that within the next 25 years we will know the genome for most living organisms as well as how they function, how they have evolved over time and how they interact with one another. This is a new era of informational biology, which will allow us to understand all living organisms.

The key issue: is society ready?

The paradox, as seen by Philippe Rigault, is that as knowledge is being built and solutions are developed, there is resistance in Western societies as some people seek to halt development or even take a step backwards. Some people view any human intervention in a natural process as heresy. This applies to all new endeavours, specifically and preferably relating to others, since the proponents of these schools of thought will rarely shun vaccines, antibiotics, infertility treatments, fruits and vegetables developed through select genetic modifications since the Neolithic period (like the sweet potato), hydroelectricity or other technology contributing to their modern-day comforts.

In dealing with the major issues of tomorrow confronting the human race today, innovators like Philippe Rigault are boldly seeking solutions while trying to understand how to improve living organisms through technology. These researchers do not fear the world that awaits us and believe that it must be adapted quickly so that we may continue to live better, and in a sustainable manner.  The conclusion of their analysis is that the solution involves using technology to address the functions of living organisms in order to improve natural and artificial ecosystems and to tailor these ecosystems to new realities and have a new management plan for the planet following a social debate informed by this new knowledge.

The challenges before us are urgent and must be addressed simultaneously and on a global scale. However, they cannot be resolved by taking a step backwards. What solution will society choose? This question is compelling, to say the least, and warrants consideration and debate.

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