npj Genomic Medicine (Nov 2022)

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 Blom,
  • Ronny Derks,
  • Menno Tjon-Pon-Fong,
  • Helger G. Yntema,
  • Marcel R. Nelen,
  • Lisenka E.L.M. Vissers,
  • Dorien Lugtenberg,
  • Kornelia Neveling

DOI
https://doi.org/10.1038/s41525-022-00334-9
Journal volume & issue
Vol. 7, no. 1
pp. 1 – 10

Abstract

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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.