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Using the Phenome and Genome to Improve Genetic Diagnosis for Deafness

The advent of massively parallel sequencing (MPS) has revolutionized genetic testing for deafness by enabling personal genomics in diagnosis (for a comprehensive review, see Shearer et al1). This technology has drastically increased the throughput of genetic testing but concomitantly has exponentially increased the amount of genetic data generated. To address this deluge of data and to streamline analysis, we have developed a custom variant prioritization pipeline incorporating data from a patient’s genome and phenome (the patient’s phenotype). In aggregate, the patient’s phenome is his or her constellation of phenotypic traits, which for hearing loss includes the patien’s audioprofile (pattern of hearing loss on audiogram), temporal bone anatomy (imaging), and ocular pathology (fundoscopy). Here we present 3 cases to illustrate how knowledge of a patient’s phenome can assist variant prioritization by corroborating likely pathogenic variants and excluding variants of unknown significance (VUS).