title: An integrative pipeline for multi-modal discovery of disease relationships.
abstract: In the past decade there has been an explosion in genetic research that has resulted in the generation of enormous quantities of disease-related data. In the current study, we have compiled disease risk gene variant information and Electronic Medical Record (EMR) classification codes from various repositories for 305 diseases. Using such data, we developed a pipeline to test for clinical prevalence, gene-variant overlap, and literature presence for all 46,360 unique diseases pairs. To determine whether disease pairs were enriched we systematically employed both Fishers' Exact (medical and literature) and Term Frequency-Inverse Document Frequency (genetics) methodologies to test for enrichment, defining statistical significance at a Bonferonni adjusted threshold of (p < 1 × 10(-6)) and weighted q < 0.05 accordingly. We hypothesize that disease pairs that are statistically enriched in medical and genetic spheres, but not so in the literature have the potential to reveal non-obvious connections between clinically disparate phenotypes. Using this pipeline, we identified 2,316 disease pairs that were significantly enriched within an EMR and 213 enriched genetically. Of these, 65 disease pairs were statistically enriched in both, 19 of which are believed to be novel. These identified non-obvious relationships between disease pairs are suggestive of a shared underlying etiology with clinical presentation. Further investigation of uncovered disease-pair relationships has the potential to provide insights into the architecture of complex diseases, and update existing knowledge of risk factors.
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl. New York City, NY 10029, USA.
authors.forename: Benjamin S
authors.initials: BS
authors.lastname: Glicksberg
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Wei-Yi
authors.initials: WY
authors.lastname: Cheng
authors.forename: Khader
authors.initials: K
authors.lastname: Shameer
authors.forename: Jörg
authors.initials: J
authors.lastname: Hakenberg
authors.forename: Rafael
authors.initials: R
authors.lastname: Castellanos
authors.forename: Meng
authors.initials: M
authors.lastname: Ma
authors.forename: Lisong
authors.initials: L
authors.lastname: Shi
authors.forename: Hardik
authors.initials: H
authors.lastname: Shah
authors.forename: Joel T
authors.initials: JT
authors.lastname: Dudley
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic / Q000706:statistics & numerical data; D004194:Disease / Q000235:genetics*; D057286:Electronic Health Records; D063990:Gene Ontology / Q000706:statistics & numerical data; D005819:Genetic Markers; D014644:Genetic Variation; D006801:Humans; D009154:Mutation; D010641:Phenotype; D012307:Risk Factors
chemical_list: D005819:Genetic Markers