Pathway networks generated from human disease phenome

BACKGROUND: Understanding the effect of human genetic variations on disease can provide insight into phenotype-genotype relationships, and has great potential for improving the effectiveness of personalized medicine. While some genetic markers linked to disease susceptibility have been identified, a large number are still unknown. In this paper, we propose a pathway-based approach to extend disease-variant associations and find new molecular connections between genetic mutations and diseases. METHODS: We used a compilation of over 80,000 human genetic variants with known disease associations from databases including the Online Mendelian Inheritance in Man (OMIM), Clinical Variance database (ClinVar), Universal Protein Resource (UniProt), and Human Gene Mutation Database (HGMD). Furthermore, we used the Unified Medical Language System (UMLS) to normalize variant phenotype terminologies, mapping 87% of unique genetic variants to phenotypic disorder concepts. Lastly, variants were grouped by UMLS Medical Subject Heading (MeSH) identifiers to determine pathway enrichment in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. RESULTS: By linking KEGG pathways through underlying variant associations, we elucidated connections between the human genetic variant-based disease phenome and metabolic pathways, finding novel disease connections not otherwise detected through gene-level analysis. When looking at broader disease categories, our network analysis showed that large complex diseases, such as cancers, are highly linked by their common pathways. In addition, we found Cardiovascular Diseases and Skin and Connective Tissue Diseases to have the highest number of common pathways, among 35 significant main disease category (MeSH) pairings. CONCLUSIONS: This study constitutes an important contribution to extending disease-variant connections and new molecular links between diseases. Novel disease connections were made by disease-pathway associations not otherwise detected through single-gene analysis. For instance, we found that mutations in different genes associated to Noonan Syndrome and Essential Hypertension share a common pathway. This analysis also provides the foundation to build novel disease-drug networks through their underlying common metabolic pathways, thus enabling new diagnostic and therapeutic interventions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12920-018-0386-2) contains supplementary material, which is available to authorized users.