Long-Read Sequencing Increases Diagnostic Yield for Pediatric Sensorineural Hearing Loss

The diagnostic yield of genetic testing for pediatric sensorineural hearing loss (SNHL) has remained at around 40% for over a decade despite newly discovered causative genes and the expanded use of exome sequencing (ES). This stagnation may be due to (1) a focus on coding regions of the genome and (2) an inability to resolve variants in complex genomic regions due to reliance on short-read sequencing technologies. Short-read genome sequencing (srGS) and long-read genome sequencing (lrGS) both provide exonic single nucleotide variant (SNV) and small indel detection at the same sensitivity as ES, but also evaluate intronic regions. lrGS provides improved resolution for structural variants (SV) and repetitive genomic regions. We sought to investigate the potential utility of lrGS in the diagnostic evaluation of a small cohort of patients with SNHL of unknown etiology after ES and srGS. 19 pediatric patients with SNHL underwent lrGS via PacBio SMRT sequencing. Sequencing data were processed using the PacBio WGS variant pipeline. The diagnostic yield for this lrGS cohort was 4/19 (21%). Relevant variants detected only with lrGS included a hemizygous deletion in trans with a missense variant in an area of high genomic homology (OTOA) and two single nucleotide loss-of-function variants in trans to a known copy-number-loss for a gene with a highly homologous pseudogene (STRC). A complex inversion was identified in the MITF gene which was also identified on post-hoc analysis by srGS. LrGS provides improved resolution for complex genomic structural variation which may increase diagnostic yield for genetic pediatric SNHL, and, potentially, rare disease more broadly.