Personalized Medicine

DNA sequencing technology has evolved by several orders of magnitude in the last decades and human genome sequencing at $1,000 is now a feasible reality. High-throughput data has never been so accessible, opening to many new ways in both research and clinical practice. In this context, our overarching goal is to provide new insights in the field of genome interpretation, investigating how genetic data can be used to find specific disease mechanisms and identify ad-hoc, personalized treatments. Several examples of personalized medicine have been already translated in clinical routine, however these cases are mostly limited to monogenic diseases and a greater effort in order to realize the potential of personalized medicine is still required, especially for complex phenotypes.
The Critical Assessment of Genome Interpretation (CAGI) is a community effort to evaluate the state-of-the-art in relating genetic information to phenotype. CAGI assesses current computational methods for interpreting genomic data, highlight innovations & progress, and broadly disseminate the results. Challenges are constructed from unpublished datasets provided by collaborating academic, commercial and clinical laboratories. Phenotype predictions are made by academic and commercial groups without knowledge of the experimental answers. Prediction performance is evaluated by independent assessors. Over the first five CAGI editions we participated as predictors, data providers and assessors. Participation in this experiment allowed us to face the strengths and weaknesses of the personalized medicine field at 360 degree. Top performance has been achieved by our prediction tools in Crohn’s disease and Bipolar disorder challenges among the others.
Another project associated with this topic is the Italian instance of the COVID-19 Data Portal, a reference point for the adoption of best practices and the FAIRification of COVID-19 data and research generated at national level. The Portal gathers and describes resources and services (e.g., guidelines, data repositories) that researchers and other data producers can use to make their data Findable, Accessible, Interoperable and Re-usable focusing on four broad areas: genomics, protein data, imaging data and health data.
The Portal hosts a dedicated help desk managed by ELIXIR-IT experts providing support in the deposition of COVID-19 data to the appropriate repositories. In this initiative we contribute as Project Coordinators providing the experience gathered in the management of international projects within the EC funding frameworks and ensuring coordination with the ELIXIR infrastructure at European level.