Scientists and clinical staff together to become an excellence in precision medicine

Sharing the fundamental scientific knowledge and practices for the creation of a personalized and precision medicine center closely connected with regional hospitals, so as to become a unique reality at national and European level. With this aim, a scientific workshop between researchers of the project was held on 13 and 14 May 5000 genomes @ VdA and the clinical staff of the Aosta Valley AUSL.

ManuelaVecchi audience
ManuelaVecchi audience

The meeting came after the Ethics Committee approved the experimental protocols of the 5000genomi @ VdA project and the researchers started sequencing the first genomes of patients being treated at the regional hospital “Umberto Parini” in Aosta.

Thanks to the 5000genomi @ VdA project he was born in Aosta a new center for genomic analysis and big data, the Center for Personalized, Preventive and Predictive Medicine (CMP3VdA), bringing together multidisciplinary expertise, with a focus on genomics and artificial intelligence. Located in the Espace Aosta Area, the CMP3VdA spread over an area of ​​laboratories of more than 450sqm completed in the first half of 2021 and divided into two departments, Medical Genomics and Computational Genomics, equipped with state-of-the-art equipment.

Aosta genomes center
5000genomi @ VdA – Author: G.Berretta
Credits: Italian Institute of Technology – © IIT, all rights reserved

The project is the result of the work of the research consortium led by the IIT-Italian Institute of Technology and composed ofUniversity of Valle d’Aosta, the City of Health and Science of Turin, the Clément Fillietroz Foundation-ONLUS Astronomical Observatory of the Valle d’Aosta Autonomous Region and Engineering D.HUB. The project is also supported by the Autonomous Region of Valle d’Aosta with European Union structural funds (ERDF and ESF) equal to 10.6 million euros in 5 yearsand 9.5 million in co-financing by the consortium.

The project aims at study the genome of about 400 children with autism spectrum disorders and other cognitive disorders, to investigate their genetic origin and improve both early diagnosis systems and possible treatments, and 2000 patients with Alzheimer’s or Parkinson’s disease in order to identify known causative or genomic variants susceptibility for neurodegenerative diseases. In the case of tumors, about 800 cases of cancer patients will be studied with the aim of developing a new personalized genomic panel for genetic alterations affecting the Valle d’Aosta population. In the case of transplants, approximately 200 patients will be analyzed in order to identify genomic variants not yet recognized as a cause or susceptibility factor for diseases treatable with transplantation.

Alessandro Coppe coord of the Computational Genomics Department
Alessandro Coppe coord of the Computational Genomics Department

Despite the slowdown due to the pandemic, in the last three months the scientific staff of the CMP3VdA together with the AUSL clinical staff have already identified the first cancer patients, who have agreed to voluntarily join the genomic in-depth studies. These studies will represent, together with future analyzes, a source of information on the specificity of certain tumors and on the possible presence of common traits within the Valle d’Aosta population.

The reading of the genomes takes place via the use of the Illumina NovaSeq 6000 sequencera next generation sequencer (NGS – Next Generation Sequencing) that it has the ability to read the entire genome of approximately 60 samples in less than 44 hours and has several useful applications for numerous research activities on both DNA and RNA.

Horses Christille Gardens
Horses Christille Gardens

The analysis of genomic data, on the other hand, is possible thanks to bioinformatics programs supported on an advanced computing infrastructure. The CMP3VdA, in fact, is equipped with a center of High Performance Computing (HPC) located at the Pont-Saint-Martin headquarters of the partner company Engineering D.HUB of the Engineering Group. The HPC is made up of 12 computational nodes (CPU, GPU and FAT CPU) and a 100TB high performance storage system. All data collection and storage processes are guaranteed by strict European and international standards, which also provide for a double saving of the same in an additional Engineering D.HUB data center located in Vicenza.

The project also provides the realization of the genomic study of some specificities of the regional territory in collaboration with local authorities, forming a real territorial network for the investigation of flora, fauna, cultural heritage and food and wine products. Among the entities also the Gran Paradiso National Park, whose collaboration is leading to the sequencing of the genome of the ibex, an animal symbol of the Park and uniqueness of the Aosta Valley fauna.

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