Chiara Beatrice Salvemini

Background: Precision medicine (PM) considers the genetic variability of individuals to identify tailored diagnosis and treatments. It relies on the possibility of gathering the widest possible health data and genetic information from individuals to obtain a broad pool of comparative data. To achieve this goal, the Region of Valle d’Aosta, since 2019, has co-financed the research center CMP³VdA, aiming to sequence 5000 genomes of patients with neurodevelopmental, neurodegenerative, oncological, and organ transplantation diseases, and to investigate the genetic variability of the resident population. Methods: This paper presents the results of an online survey of 472 (328F) respondents regarding willingness to participate in the genomic project and awareness, attitudes, and concerns about PM. Results: The main results show that the vast majority (92.6%) would be willing to participate—a higher percentage than in previous studies. Age, education, and prior experience in the healthcare sector are significant factors influencing the awareness of PM. Additionally, subgroups organized by age, gender, and religiosity show significant differences with respect to participants’ reasons for participating in research and which types of biological samples they would be willing to donate. Conclusions: Our findings can serve as a guide for stakeholders—particularly policymakers—to target institutional communication and achieve maximum participation in genomic research projects.

Advances in next-generation sequencing have provided high-dimensional RNA-seq datasets, allowing the stratification of some tumor patients based on their transcriptomic profiles. Machine learning methods have been used to reduce and cluster high-dimensional data. Recently, uniform manifold approximation and projection (UMAP) was applied to project genomic datasets in low-dimensional Euclidean latent space. Here, we evaluated how different representations of the UMAP embedding can impact the analysis of breast cancer (BC) stratification. We projected BC RNA-seq data on Euclidean, spherical, and hyperbolic spaces, and stratified BC patients via clustering algorithms. We also proposed a pipeline to yield more reproducible clustering outputs. The results show how the selection of the latent space can affect downstream stratification results and suggest that the exploration of different geometrical representations is recommended to explore data structure and samples’ relationships.