Long-read technologies identify a hidden inverted duplication in a family with choroideremia
Zeinab Fadaie,
Kornelia Neveling,
Tuomo Mantere,
Ronny Derks,
Lonneke Haer-Wigman,
Amber den Ouden,
Michael Kwint,
Luke O’Gorman,
Dyon Valkenburg,
Carel B. Hoyng,
Christian Gilissen,
Lisenka E.L.M. Vissers,
Marcel Nelen,
Frans P.M. Cremers,
Alexander Hoischen,
Susanne Roosing
Affiliations
Zeinab Fadaie
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
Kornelia Neveling
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
Tuomo Mantere
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
Ronny Derks
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
Lonneke Haer-Wigman
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
Amber den Ouden
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
Michael Kwint
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
Luke O’Gorman
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
Dyon Valkenburg
Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
Carel B. Hoyng
Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
Christian Gilissen
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
Lisenka E.L.M. Vissers
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
Marcel Nelen
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
Frans P.M. Cremers
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
Alexander Hoischen
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Corresponding author
Susanne Roosing
Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Corresponding author
Summary: The lack of molecular diagnoses in rare genetic diseases can be explained by limitations of current standard genomic technologies. Upcoming long-read techniques have complementary strengths to overcome these limitations, with a particular strength in identifying structural variants. By using optical genome mapping and long-read sequencing, we aimed to identify the pathogenic variant in a large family with X-linked choroideremia. In this family, aberrant splicing of exon 12 of the choroideremia gene CHM was detected in 2003, but the underlying genomic defect remained elusive. Optical genome mapping and long-read sequencing approaches now revealed an intragenic 1,752 bp inverted duplication including exon 12 and surrounding regions, located downstream of the wild-type copy of exon 12. Both breakpoint junctions were confirmed with Sanger sequencing and segregate with the X-linked inheritance in the family. The breakpoint junctions displayed sequence microhomology suggestive for an erroneous replication mechanism as the origin of the structural variant. The inverted duplication is predicted to result in a hairpin formation of the pre-mRNA with the wild-type exon 12, leading to exon skipping in the mature mRNA. The identified inverted duplication is deemed the hidden pathogenic cause of disease in this family. Our study shows that optical genome mapping and long-read sequencing have significant potential for the identification of (hidden) structural variants in rare genetic diseases.