Diagnostic analysis of the highly complex OPN1LW/OPN1MW gene cluster using long-read sequencing and MLPA
Lonneke Haer‐Wigman, Amber den Ouden, Maria M. van Genderen, Hester Y. Kroes, Joke Verheij, Dzenita Smailhodzic, Attje S. Hoekstra, Raymon Vijzelaar, Jan Dirk Blom, Ronny Derks, Menno Tjon-Pon-Fong, Helger G. Yntema, Marcel Nelen, Lisenka E.L.M. Vissers, Dorien Lugtenberg, Kornelia Neveling
Abstract
Pathogenic variants in the OPN1LW/OPN1MW gene cluster are causal for a range of mild to severe visual impairments with color deficiencies. The widely utilized short-read next-generation sequencing (NGS) is inappropriate for the analysis of the OPN1LW/OPN1MW gene cluster and many patients with pathogenic variants stay underdiagnosed. A diagnostic genetic assay was developed for the OPN1LW/OPN1MW gene cluster, consisting of copy number analysis via multiplex ligation-dependent probe amplification and sequence analysis via long-read circular consensus sequencing. Performance was determined on 50 clinical samples referred for genetic confirmation of the clinical diagnosis (n = 43) or carrier status analysis (n = 7). A broad range of pathogenic haplotypes were detected, including deletions, hybrid genes, single variants and combinations of variants. The developed genetic assay for the OPN1LW/OPN1MW gene cluster is a diagnostic test that can detect both structural and nucleotide variants with a straightforward analysis, improving diagnostic care of patients with visual impairment.