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Table 1 Clinical cases causative gene rank

From: Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology

Gene Terms HPO sim score rank HPO p-value rank Variant gene set Gene set sim score rank Gene set p-value rank
USH2A 2 12 38 113 2 1
CDH23 6 32 24 125 4 3
SLC26A4 4 1 26 135 1 1
GJB2 3 44 218 129 4 16
  1. Causative gene ranks for patients with hearing impairment. Gene: the causative gene for each case. Terms: the number of HPO phenotype terms assigned to the subject by the genetic counselor. HPO Sim Score Rank: the calculated causative gene rank using the semantic similarity score compared to all 2,488 HPO annotated genes. HPO p-value Rank: the calculated causative gene rank using the p-value compared to all 2,488 HPO annotated genes. Variant Gene Set: the number of genes with variants identified in the patient of interest. The variant gene set represents genes for which the patient had exonic or splice site variants that occur with a minor allele frequency: <10% in CHOP’s internal cohort or <3% in exomes from either the 1000 Genomes Project [23] or the NHLBI Exome Variant Server [24]. Gene Set Sim Score Rank: the calculated causative gene rank using the semantic similarity score when compared to the subset of genes included in that patient’s variant gene set. Gene Set p-value Rank: the calculated causative gene rank using the p-value when compared to the subset of genes included in that patient’s variant gene set.