LINE‐1 insertion in the RP1 gene in a family with retinitis pigmentosa

Abstract

AbstractPurpose: A family, with dominantly inherited retinal dystrophy in three generations, was negative for alterations in known causative genes upon initial analysis. We aimed to identify the causative pathogenic germline variant.Methods: Two of the six affected members were treated in the Helsinki University Hospital. The patients were subjected to clinical examination and retinal imaging, and the DNA samples to exome sequencing. The variants were called from the sequencing reads using Illumina DRAGEN™ Bio‐IT Platform. The identified pathogenic variant was visualized using Integrative Genomics Viewer (IGV) and confirmed by PCR and Oxford nanopore adaptive sequencing.Results: Two of the family members had typical retinitis pigmentosa with narrowed visual fields, peripheral retinal bone spicules, and cystic or atrophic changes in the macula. DRAGEN™ identified a LINE‐1 insertion in exon 4 of RP1 from the index that was also found in the cousin upon closer IGV inspection. The 5′‐end of the LINE‐1 insertion was confirmed by PCR using primers targeting the LINE‐1 fragment and RP1 exon 4 upstream of the suspected insertion site. However, PCR amplification over the LINE‐1 insertion was unsuccessful, indicating a considerably larger insertion than the 54‐bases called by DRAGEN™. Thus, Oxford nanopore adaptive sequencing will be used to resolve the true size and the breakpoints of the insertion.Conclusions: We report here that the retinitis pigmentosa of previously unresolved origin is caused by insertion of LINE‐1 transposon in the RP1 gene. Furthermore, NGS variant‐calling algorithms do not always detect aberrations from moving elements.