Predicting genes from phenotypes using human phenotype ontology (HPO) terms

The interpretation of genomic variants following whole exome sequencing (WES) can be aided using human phenotype ontology (HPO) terms to standardize clinical features and predict causative genes. We performed WES on 453 patients diagnosed prior to 18 years of age and identified 114 pathogenic (P) or likely pathogenic (LP) variants in 112 patients. We utilized PhenoDB to extract HPO terms from provider notes and then used Phen2Gene to generate a gene score and gene ranking from each list of HPO terms. We assigned Phen2Gene gene rankings to 6 rank classes, with class 1 covering raw gene rankings of 1 to 10 and class 2 covering rankings from 11 to 50 out of a total of 17,126 possible gene rankings. Phen2Gene ranked causative genes into rank class 1 or 2 in 27.7% of cases and the genes in rank class 1 were all associated with well-characterized phenotypes. We found significant associations between the gene score and the number of years, since the gene was first published, the number of HPO terms with an hierarchical depth greater or equal to 11, and the number of Online Mendelian Inheritance in Man terms associated with the phenotype and gene. We conclude that genes associated with recognizable phenotypes and terms deep in the HPO hierarchy have the best chance of producing a high gene score and ranking in class 1 to 2 using Phen2Gene software with HPO terms. Clinicians and laboratory staff should consider these results when HPO terms are employed to prioritize candidate genes.