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:10.1038/s41525-022-00334-9

Diagnostic analysis of the highly complex OPN1LW/OPN1MW gene cluster using long-read sequencing and MLPA

NPJ Genom Med. 2022 Nov 9;7(1):65. doi: 10.1038/s41525-022-00334-9.

Authors

Lonneke Haer-Wigman^{1

2}, Amber den Ouden³, Maria M van Genderen^{4

5}, Hester Y Kroes⁶, Joke Verheij⁷, Dzenita Smailhodzic^{4

8}, Attje S Hoekstra⁹, Raymon Vijzelaar⁹, Jan Blom³, Ronny Derks³, Menno Tjon-Pon-Fong^{3

10}, Helger G Yntema^{3

10}, Marcel R Nelen³, Lisenka E L M Vissers^{3

10}, Dorien Lugtenberg^{3

10}, Kornelia Neveling^{3

10}

Affiliations

¹ Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. lonneke.haer-wigman@radboudumc.nl.
² Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands. lonneke.haer-wigman@radboudumc.nl.
³ Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
⁴ Bartiméus Diagnostic Center for complex visual disorders, Zeist, The Netherlands.
⁵ Department of Ophthalmology, University Medical Centre Utrecht, Utrecht, The Netherlands.
⁶ Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
⁷ Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
⁸ The Rotterdam Eye Hospital, Rotterdam, 3011 BH, The Netherlands.
⁹ MRC Holland b v, Amsterdam, The Netherlands.
¹⁰ Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.

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.