Examples of application of genomics and epigenomics

Impulse for the development of new generation diagnostic, prognostic and predictive tools. Raw material analysis and environmental monitoring

The platform may become a reference centre to which researchers and companies can turn for sequencing analysis in order to develop:

• Genetic tests. Using new-generation sequencing platforms, it is now possible to analyse the entire genetic code of individual genomes, contributing to the increase of knowledge of human diseases and providing a strong impetus for the development of new-generation diagnostic, prognostic and predictive tools. It is also possible to develop genetic tests based on the analysis in a single test of one or more human genes (coding portions), which may have different purposes: diagnostic and presymptomatic tests traditionally used to identify rare diseases; predictive tests to identify genomic variants associated with a greater or lesser vulnerability to common diseases (e.g. cardiovascular diseases); pharmacogenetic tests to assess the individual response to pharmacological treatment; tests to identify healthy carriers of genetically-determined conditions.
• Study of microorganisms to investigate how they affect human diseases. By sequencing thousands of organisms in parallel (metagenomics), the NGS has revolutionised microbiology by allowing the simultaneous analysis of entire microbial communities and the identification of strains that might not be identifiable using other methods. In the future, the microbiota sequencing test may be implemented as part of normal clinical and diagnostic practice for certain diseases or increased susceptibility to certain disorders. In addition, the sequencing of bacterial genomes permits the analysis of genes involved in antibiotic resistance, allowing the development and optimisation of new therapeutic options for infectious diseases.
• Analysis on plants, animals, invertebrates and microorganisms, in order to further the knowledge of genomes of organisms less-studied than humans, or not yet characterised, especially with regard to organisms of zootechnical or agronomic interest. Understanding the structure, function and genetic diversity of the genomes of cultivated plants or farm animals enables the optimisation of their selection efficiency and of the productivity, quality and safety of the products. For plant species, knowledge about the agronomic characteristics derived from the genomic approach (efficiency in the use of water, nitrogen, phosphorus, resistance to biotic stress and environmental changes) allows them to be adapted to the changing needs of the consumer (safer foods, higher quality and nutritional value) and of society (plants as energy sources and other non-food products). Genomic analysis in animal husbandry provides information for the selection of farm animals with rapid growth and resistance to disease and for the investigation of genetic kinships between animal species and breeds.
• Analysis of the traceability of the agro-food chain and environmental monitoring. Through the metagenomic approach applied to DNA extracted from food and environmental samples of various origins (e.g. soil, wastewater, sea) it is possible to detect any contamination in raw materials, food and environmental matrices. The genetic traceability of agri-food products makes it possible to verify the origin of raw materials and derived products for food use, monitor their production and enhance their quality, in order to protect the consumer against fraud. On the other hand, environmental monitoring is essential to detect contamination and ensure environmental biodiversity.
• Study of epigenetic mechanisms and genotype-environment interaction. The investigation of the epigenetic regulation of genes, through the analysis of the chemical alterations of DNA that do not affect the sequence or the modifications of proteins that are associated with DNA, has interesting applications in both the biomedical and agri-food sectors. The alterations of the epigenetic program are, in fact, directly involved in numerous diseases such as diabetes, degenerative neuromuscular diseases, viral infections and cancer, as well as in the mechanisms that regulate the mechanisms related to circadian rhythms and adaptation to the environment. This has profound implications for the understanding of the biodiversity of each individual (e.g. the different expression of phenotypes and individual responses to certain drugs), also of an ecological nature where epigenetic profiles are specific to particular conditions of growth, development and adaptation of living beings. In addition, using a high-throughput NGS platform it would be possible to explore the mechanisms leading to the creation of new epigenetic variability in plants to implement genetic improvement programs aimed at increasing resistance to environmental stresses that do not require direct intervention on the genome of the organism.