Targeted long-read nanopore sequencing as a complementary approach for detecting STRC variants and distinguishing the STRCP1 pseudogene

The stereocilin (STRC) gene is a significant contributor to mild-to-moderate sensorineural hearing loss (SNHL), particularly in cases of biallelic STRC deletions and copy number alterations. Although pathogenic single nucleotide variants (SNVs) or small insertion-deletions (indels) have been investigated across the coding region of STRC, the pseudogene STRCP1, which shares 98% homology with the STRC gene, makes interpreting sequence data from this region challenging. To detect missing SNVs, targeted long-read sequencing was conducted using the nanopore MinION platform coupled with long-range polymerase chain reaction (PCR) enrichment on individuals exhibiting heterozygous STRC deletions and associated phenotypes. Sequencing results were obtained from 149 DNA samples. The median number of reads and depth of coverage were 4,088 and 2,780, respectively. The average read length of 20.76 kbp corresponded to that of a long-range PCR product, indicating precise analysis using MinION. Forty-three individuals carrying SNVs or small indels and 27 variants were identified. Thirteen were previously reported as hearing loss-causing variants and 14 were novel variants. Long-read sequencing technology enables precise detection of pathogenic variants in complex genomic regions, such as STRC, where conventional methods face challenges owing to pseudogene interference. Therefore, this approach is a valuable complement to conventional methods for resolving unresolved SNHL. This study demonstrates the utility of targeted long-read sequencing as a complementary method to short-read NGS for resolving complex regions such as STRC. The combination with long-range PCR enabled precise enrichment and improved resolution in SNV detection.