Navigome: Navigating the Human Phenome

Abstract

We now have access to a sufficient number of genome-wide association studies (GWAS) to cluster phenotypes into genetic-informed categories and to navigate the \"phenome\" space of human traits. Using a collection of 465 GWAS, we generated genetic correlations, pathways, gene-wise and tissue-wise associations using MAGMA and S-PrediXcan for 465 human traits. Testing 7267 biological pathways, we found that only 898 were significantly associated with any trait. Similarly, out of ~20,000 tested protein-coding genes, 12,311 genes exhibited an association. Based on the genetic correlations between all traits, we constructed a phenome map using t-distributed stochastic neighbor embedding (t-SNE), where each of the 465 traits can be visualized as an individual point. This map reveals well-defined clusters of traits such as education/high longevity, lower longevity, height, body composition, and depression/anxiety/neuroticism. These clusters are enriched in specific groups of pathways, such as lipid pathways in the lower longevity cluster, and neuronal pathways for body composition or education clusters. The map and all other analyses are available in the Navigome web interface (https://phenviz.navigome.com).