Characterization of STRC Gene Conversions by Nanopore Sequencing

Biallelic loss-of-function variants of STRC are a frequent cause of mild to moderate nonsyndromic hearing loss. The high (>98%) sequence homology between STRC and its pseudogene STRCP1 poses a significant challenge for accurate interpretation of STRC variants using standard methods. Although STRC-STRCP1 gene conversions have frequently been inferred from next-generation sequencing and copy number variant analysis data, their structure remains poorly delineated. We employed long-read sequencing to characterize the breakpoints of STRC-STRCP1 gene conversions.

Three specimens with suspected STRC-STRCP1 gene conversions were analyzed by Nanopore sequencing. Long-range PCR was employed to selectively amplify the rearranged alleles, using 2 different primer pairs based on the predicted gene-conversion structures.

Nanopore sequencing data confirmed that segments of the wild-type STRC gene were replaced by the corresponding STRCP1 regions in the amplified alleles, consistent with a gene-conversion mechanism in all 3 specimens. Detailed analysis of mismatch patterns, obtained by aligning long reads to reference sequences, further clarified the extent of these conversions. One specimen showed replacement of STRC exons 12 to 23 by STRCP1 sequences, while the other 2 revealed gene conversions involving the terminal STRC exons extending into the adjacent CKMT1B gene. Breakpoints were mapped with variable resolution depending on the rearrangement characteristics.

Our approach successfully overcomes the resolution limitations of conventional techniques, providing the molecular characterization of STRC-STRCP1 gene conversions. These findings underscore the clinical relevance of such events and highlight the diagnostic potential of Nanopore sequencing in genetic testing.